2 
Characterization of Biodiversity 
FA. BISBY 
Lead Authors: 
F.A. Bisby and J. Coddington (Chapter 2.1); J.P Thorpe, J. Smartt (Chapter 2.2); 
R. Hengeveld, P.J. Edwards, S.J. Duffield (Chapter 2.3) 
Contributors: 
/. Cracraft, D.L. Hawksworth, D. Lipscomb, N.R. Morin, P. Munyenyembe, G.J. Olsen, 
D.LJ. Quiche, MM. V van Regenmortel, Y.R. Rostov (Chapter 2.1); A.L Alkock, 
M. Chauvet, K.A. Crandall, D.R. Given, S.J.G. Hall, J.M. Iriondo, T.M. Lewinsohn, 
S.M. Lynch, G.M. Mace, A.M. Sole-Cava, E. Stackebrandt, A.R. Templeton, RC. Watts 
(Chapter 2.2); M.T. Kalin-Arroyo, J. Bullock, R.G.H. Bunce, E.A. Norse, A. Magurran, 
K. Natarajan, S.L Pimm, R.E. Ricklefs (Chapter 2.3) 
CONTENTS 
Elective Summary 25 
2.0 Introduction to the characterization of biodiversity 27 
2.0.1 What is biodiversity? 27 
2.0.2 What components of biodiversity are to be 
characterized? 27 
2.0.3 What is meant by characterizing biodiversity? 27 
2.1 Biodiversity from a taxonomic and evolutionary 
perspective 27 
2.1.0 Introduction: patterns of living organisms - 
classification and evolution 27 
2.1,0.1  Folk classifications and the origin of 
scientific taxonomy 29 
2 1.1 The basics of taxonomic characterization: 
what taxonomists do 31 
2.1.1.1 The role of specimens in taxonomy 31 
2.1.1.2 Stability of scientific names 33 
2.1.2 Characterizing flora, fauna and microbiota: 
preparing Floras, handbooks and keys 33 
2.1.2.1 The amount of research work involved 34 
2.1.2.2 Modem developments: databases and 
expert identification systems 35 
2.1.3 Characterizing systematic patterns: the species, 
their evolution and their classification 36 
2.1.3.1 Analysing systematic data to reconstruct 
evolutionary history 36 
2.1.3.2 From phylogenetic trees to formal 
classifications 38 
2.1.3.3 Why do classification schemes change? 38 
2.1.4 Charac;enzing species 40 
2.1.4.1 The morphological species concept 41 
2.1.4.2 The biological species concept 41 
2.1.4.3 The phylogenetic species concept 43 
2.1.4.4 The pluralistic approach 44 
2.1.5 The power of taxonomy and taxonomic products 46 
2.1.5.1 Taxonomic products: an essential 
technological infrastruciure for 
biotechnology, natural resources 
management, and regulation 46 
2.1.5.2 As a summary of biodiversity and 
evoluiionary patterns 47 
2.1.5.3 As a basis for prediction 49 
2.1.5.4 Other uses of taxonomic techniques 50 
' ? Taxonomic measures of species diversity 51 
2.1.6.1 Evaluating taxonomic isolation of 
individual species 51 
2.1.6.2 Measuring taxonomic diversity of biota 
or ecosystems 53 
2.1,7 Conclusion 53 
References 53 
2.2 Genetic diversity as a component of biodiversity 57 
2.2.0 Introduction 57 
2.2.1 Partitioning of genetic variability below the 
species level 61 
2.2.1.1 Analysis of karyotypic variation 63 
2.2.1.1.1 Karyotypic variation analysis 
techniques 63 
2.2.1.1.2 Genetic diversity studies 63 
2.2.1.1.3 Assessment 64 
2.2.1.2 Molecular methods for assessing levels 
of genetic diversity 65 
2.2.1.2.!   Allozymes 65 
2.2.1.2.2 Restriction fragment length 
polymorphism (RFLP) 67 
2.2.1.2.3 Multi-locus DNA fingerprinting 
of minisatellite loci 68 
2.2.1.2.4 Single-locus DNA fingerprinting 
of minisatellite loci 68 
2.2.1.2.5 Gene cloning and poly me rase 
chain reaction (PCR) 68 
2.2.126 Nucleotide sequences 69 
2.2.1.2.7 Applications of PCR 69 
2.2.1.2.8 Conclusions 69 
2.2.2 Patterns of differentiation under domestication 70 
2.2.2.1   Characterizing biodiversity within 
domesticated species 73 
2 2 2 2 The genetic basis of cultivarsand breeds 75 
2.2.2.3 Species complexes and gene flow 76 
2.2.2.4 Future developments 77 
2.2.3 Investigating genetic diversity 77 
2.2.3.1 Type of biological material available 79 
2.2.3.2 Research and development 79 
2.2.4 Case studies of the use of genetic techniques 
in studies of wiihtn-species and between- 
species diversity 79 
2.2.4.1 Pctrtula 79 
2.2.4.2 Aiutlis 81 
References 82 
24 
\ 
Characterization of Biodiversity 
2.3 Biodiversity from an ecological perspective 
2.3.1 Introduction 
2.3.2 Diversity within areas 
2.3.2.1  Species richness and species diversity 
2.3 2.1.1  Comparing diversity across 
species groups: coherence of 
patterns 
2.3.2.1.2 Comparing areas of different 
sixes 
8S 
?SS 
'XI 
'Mi 
2.3.2.1.3 The relative abundance of species 91 
2.3.2.2 Taxic diversity 91 
2.3.2.3 Functional diversity 92 
2.3.2.3.1  Autecological diversity (species 
in isolation) 92 
2 3.2.3.2 Synecological diversity (species 
in communities) 93 
2 3.3 Diversity between areas 
2.3.3.1 The general difficulties in classifying 
ecological communities 
2.3.3.2 Classifications based on species 
composition 
2.3.3.2.1 Phytosociology 
2.3.3.2.2 Global classifications of 
species distribution 
2.3.3.3 Global classifications of ecosystems 
2.3.3.4 Characterising and classifying landscapes 
2.3.3.5 Diversity in ecological systems 
2.3.3.6 The importance of better ecological 
classifications 
2.3,4 Conclusions 
References 
<M 
94 
96 
97 
100 
102 
102 
102 
103   j 
104   \ 
#- 
EXECUTIVE SUMMARY 
. jhe recognition and characterization of biodiversity 
depends critically on the work of three scientific 
disciplines. Taxonomy provides the reference system and 
depicts the pattern or tree of diversity for all organisms 
(Chapter 2.1). Genetics gives a direct knowledge of the 
gene variations found within and between species (Chapter 
2.2). Ecology provides knowledge of the varied ecological 
systems in which taxonomic and genetic diversity is 
located, and of which it provides the functional 
components (Chapter 2.3). 
? There appear to be no short cuts to full examination 
of biodiversity. All three disciplines report in 
this assessment that, having characterized only part of 
the world's biological diversity, it will be necessary 
to undertake similar work to survey the remainder. 
While predictions can be made, they are no substitute 
for full enumeration. It is in the nature of biodiversity 
that surprises and uniqueness abound: predictive 
methods, such as the use of indicator species, 
latitudinal gradients, and mapping of hotspots, are of 
limited value, 
? Taxonomy provides the core reference system and 
knowledge-base on which all discussion of biodiversity 
hinges: the framework within which biodiversity is 
recognized and in which species diversity 
characterization occurs. The most commonly used units 
of biological diversity are species, the basic kinds 
of organisms. 
* Taxonomic characterization of the world's organisms is a 
mammoth but essential strategic task with which only 
limited progress has been made: just I 75 of the estimated 
13 to 14 million species have so far been described, and 
most of these are still poorly known in biological terms. 
There is not even a comprehensive catalogue of these 1.75 
million known species. 
* Despite its universal usage as a basic unit of taxonomy, it 
is difficult to agree on an exact definition of what 
constitutes a species. As a result there is considerable 
variation in concept and usage which may be reflected in 
differing classifications and species totals 
- Taxonomists have the task of enumerating which species 
exist and placing them in a taxonomic hierarchy. This 
taxonomic hierarchy serves both as a classification used for 
reference purposes and as a summary of the evolutionary 
tree. It can also be used to predict properties of certain 
organisms. The hierarchy is characterized by observation of 
the patterns of resemblances in comparative features such 
as morphology, anatomy, chemistry (including molecular 
data), behaviour and life-history. 
? Systematic and evolutionary studies provide valuable 
knowledge about the evolutionary origins and patterns of 
life, the scientific map of diversity. This is the map that 
must be used in planning conservation, prospecting, 
exploitation, regulation, and sustainable use. 
? It is considered important that assessments used in the 
evaluation of resources and conservation options make 
adequate use of taxic diversity measures which take into 
account not just numbers of species but their taxonomic 
positions and the differing contributions that different 
species make. The map or tree of diversity is occupied by 
very varied densities of species: in some parts there are 
thousands of species, in others just one or two. It follows 
that the very few species in certain parts of the pattern are 
of exceptionally high scientific value, 
* Genetic diversity is the diversity of the sets of genes 
carried by different organisms: it occurs not only on a small 
scale between organisms of the same population, but on a 
progressively larger scale between organisms in different 
populations of the same species, between closely related 
species such as those in the same genus, and between more 
distantly related species, those in different families, orders, 
kingdoms and domains. Genetic diversity may be 
characterized by a range of techniques: by observation of 
inherited genetic traits, by viewing under the microscope 
the chromosomes that carry the genes, and by reading the 
genetic information carried on the chromosomes using 
molecular techniques. 
* Genes transmit features from one generation to the next, 
so determining by inheritance and in interaction with the 
environment, the pattern of variation realized in features 
26 Characterization of Biodiversity 
seen within and between species. Similarly alterations in 
the genes carried forward to future generations mark the 
path of evolution. Yet scientists observe that in neither case 
is there a strictly one-to-one relationship between genetic 
diversity and the realized diversity of organisms 
characterized by taxonomists. 
zones differ taxonomically in the flora and fauna present, 
even between areas of similar physical environment (e.g. 
within the same ecoregion) or similar physiognomy (e.g. 
within the same biome). Conversely, the physiognomic 
differences between bionics within one biogeographic zone 
are para I led by those within another. 
? Genetic analysis, including molecular techniques. 
provides a formidable tool for gaining access to precise 
gene differences both within and be!ween species. Within 
species genetic details can characterise the traits and the 
populations on which natural selection and the process of 
evolution is acting. Between closely related species gene 
comparisons can reveal details of speciation and 
colonization. 
? It is selection acting on genetic diversity that carries 
forward both ecological adaptation and microevolution: to 
limit or reduce the genetic diversity within a species is to 
limit or reduce its potential or actual role in the ecological 
and evolutionary development of the biosphere. 
? The food plants, animals, fungi and other micro- 
organisms on which all humankind depend arise from 
genetic variants of originally wild organisms. The genetic 
resources in both wild and domesticated organisms thus 
represent a patrimony of resources for future use. Even the 
present well-developed food crops and animal resources are 
constantly at risk because of the rapid adaptation of pests 
and diseases: skilful and extensive manipulation of genetic 
resources is needed even to maintain agricultural 
productivity, 
? Organisms are not evenly distributed: they occur in an 
intricate spatial mosaic, classified on a world scale into 
biogeographic zones, biomes, ecoregions and oceanic 
realms, and at a variety of smaller scales within landscapes 
into ecosystems, communities and assemblages. 
? In terrestrial systems the community found at any one 
point can be characterized by the physical environment 
(ecoregion), the physiognomic type (biome), and the 
floristic/faunistic (biogeographic) zone in which it occurs 
In marine systems communities are characterized in terms 
of the physical environment and the faunistic 
(biogeographic) zone. 
? The units of classification used on a global scale differ in 
how they are recognised and consequently in the 
distinctions between their subdivisions. Biogeographic 
? All existing global classifications of ecological systems 
are to some extent inadequate, either in their methodology 
or in their spatial coverage, or in both. A robust 
classification of the world's ecosystems which can be used 
to map the distribution of ecological resources is urgently 
needed. 
? The biodiversity within an area can be characterized by 
measures of species richness, species diversity, taxic 
diversity and functional diversity - each highlighting 
different perspectives. 
(a) Species richness (also called a-diversity) measures 
the number of species within an area, giving equal 
weight to each species. 
(b) Species diversity measures the species in an area, 
adjusting for both sampling effects and species 
abundance. 
(c) Taxic diversity measures the taxonomic dispersion of 
species, thus emphasizing evolutionarily isolated 
species that contribute greatly to the assemblage of 
features or options. 
(d) Functional diversity assesses the richness of 
functional features and interrelations in an area, 
identifying food webs along with keystone species 
and guilds, characterised by a variety of measures, 
strategies and spectra. 
? A serious limitation on all measures of species diversity 
in an ecosystem is our inability to survey all organisms at 
any site: only a few taxonomic groups are sufficiently 
known for complete field surveys to be made. 
? At the smaller scale, landscapes are composed of areas 
characterised as ecosystems or communities. The diversity 
between areas is measured as (^-diversity, the change in 
species present. 
? Systems diversity is assessed as the richness of ecological 
systems in a region or landscape. 
Characterization of Biodiversity 27 
20 introduction to the characterization of biodiversity 
2.0.1 What is biodiversity? 
As explained in Section I, biodiversity means the 
variability among living organisms from all sources and the 
ecological systems of which they arc a part; this includes 
diversity within species, between species and of 
ecosystems. Were life to occur on other planets, or living 
organisms to be rescued from fossils preserved millions of 
years ago, the concept could include these as well. It can be 
partitioned, so that we can talk of the biodiversity of a 
country, of an area, or of an ecosystem, of a group of 
organisms, or within a single species. 
Biodiversity can be set in a time frame so that species 
extinctions, the disappearance of ecological associations, or the 
loss of genetic variants in an extant species can all be classed 
as losses of biodiversity. New elements of life - by mutation, 
by natural or artificial selection, by speciation or artificial 
breeding, by biotechnology, or by ecological manipulation 
- can similarly be viewed as additions to biodiversity. 
2.0.2 What is meant by characterizing biodiversity? 
The scientific characterization of biodiversity involves 
what may seem like two different processes, the 
observation and characterization of the main units of 
variation {e.g. genes, species and ecosystems), and the 
quantification of variation within and between them 
(genetic distance, taxonomic relatedness, etc.). In reality 
they are part of the same process: the analysis of pattern 
defines the units as well as characterizing their variation. 
In each of the three chapters that follow an assessment is 
made both of the reference framework and units used, and 
of the methods for quantifying variation. Chapter 2.1 deals 
with the central issue of characterizing species or 
taxonomic diversity. Chapter 2.2 assesses genetic diversity 
that occurs both within and between species. Chapter 2.3 
introduces the diversity of ecological systems in which this 
species and genetic diversity occurs, a theme further 
developed in Sections 5 and 6. 
A number of techniques described here are of wide 
application both in characterizing diversity and in topics 
addressed in later sections. The molecular techniques 
described as part of genetic diversity (Chapter 2.2) are 
widely used in taxonomic analysis (2.1) and in 
biotechnology (Section 10). The taxic diversity measures 
described in 2.1 are increasingly of interest in the 
comparison of ecological systems (2.3). No attempt is 
made to appraise cultural diversity: with its human 
and cultural dimensions, this is left until Sections 11 
and 12. 
Lastly, we should comment that this assessment of 
characterization units and techniques leaves rather a 
dissected view of biodiversity at different levels of 
description. It is for other sections to assess our knowledge 
of how the system works as a whole. 
2.1   Biodiversity from a taxonomic and evolutionary 
perspective 
This chapter contains an introduction to the taxonomic and 
evolutionary characterization biodiversity (2.1.0-2.1.4). 
This is followed by an overview of the power and utility of 
taxonomic products in general biodiversity usage (2.1.5), 
and in the particular context of species diversity assessment 
(2.1.6). 
2.1.0 Introduction: patterns of living organisms - 
classification and evolution 
The study of the different kinds of living organisms, the 
variations among and between them, how they are 
distinguished one from another, and their patterns of 
relationship, is known as taxonomy or biosystematics (see 
Box 2.1-1 for strict definitions). Taxonomy is thus 
fundamental in providing the units and the pattern to 
humankind's notion of species diversity. Indeed, the first 
estimates of global biodiversity were those made by 
taxonomists. 
At one end of the range of taxonomic studies are rather 
practical operations such as naming and cataloguing what 
kinds of organisms exist (including the preparation of 
checklists, plant Floras, animal handbooks, computerized 
identification tools, etc.), the information science aspect of 
taxonomy. At the other end are sophisticated studies of the 
branching tree and geographic patterns of evolution by 
descent (known as phytogeny) and taxonomic measures of 
biodiversity. Simple introductory texts are provided by 
Ross (1974), Jeffrey (1982), Heywood (1976) and 
Liorente-Bousquets (1990). 
Despite the sometimes bewildering complexity of forms 
observed, biosystematists have succeeded in most major 
groups in recognizing the patterns of variation and 
occurrence that are observed. The patterns can be depicted 
graphically as nested hierarchies, boxes within boxes, or 
branching trees (Figure 2.1-1) which, as we shall see later, 
can be thought of either as a nested classification or as a 
tree of descent. This practice originated simply as a human 
method of organizing knowledge, as in Aristotle's principle 
of Logical Division (Turrill 1942), where organisms are 
divided into contrasted classes: A, not A; useful, not useful; 
woody, not woody. Similarly, in Diderot's Encyclopedic 
(Diderot 1751-65) all "knowledge, including both biology 
and many other topics, is connected on a hierarchical tree 
printed inside the book's covers. But since the acceptance 
of Darwin's theory of evolution by descent with 
modification (Darwin 1859), the success of using a 
hierarchy is attributed to organisms having evolved by 
descent with modification through time, a process that 
produces a branching tree. The pattern of life actually is 
intrinsically tree-like and hierarchical in variation pattern. 
At the lowest level of this hierarchy are individual 
organisms which live and die fe.g. a particular dog, a 
28 Characterization of Biodiversity 
Box 2.1-1: Definitions of taxonomy and biosystematics. 
A distinction between taxonomy and biosystematics 
Taxonomy in the strict sense refers lo all information science aspects of handling the different sets of organisms. The 
word is sometimes used in contexts outside biology so, strictly, one should speak of biological taxonomy. Mayr 
(1969) defines it thus: 
Taxonomy is the theory and practice of classifying organisms. 
It can be thought of as having four components (Bisby 1984: Abbott el ai. 1985; R ad ford 1986: Hawksworlh and 
Bisby 1988): 
(i) the classification 
(it) the nomenclature 
(iii) circumscriptions or descriptions 
(iv) identification aids 
Biosystematics is a broader topic, which includes taxonomy, but also includes the full breadth and richness of 
associated biological disciplines, including elements of evolution, phytogeny, population genetics and biogeography 
(Hawksworth and Bisby 1988; Quicke 1993). In the late 1930s the term systematics was used in Britain to emphasize 
the move away from classical taxonomy, as in the phrase 'The New Systematics', and the establishment of 'The 
Systematics Association'. Simpson (1961) and Mayr (1969) define it thus: 
Systematics is the scientific study of the kinds and diversity of organisms and of any and all relationships among 
them. 
Again the word is used in non-biological contexts: biosystematics makes clear the biological context. 
particular tree, a particular bacterium). Individuals occur 
usually as members of more-or-less continuously existing 
populations, which can be variously characterized, 
depending on their breeding systems, either as being related 
by the process of mating amongst their immediate 
ancestors (as among humans, among beetles and among 
palm trees), or as having a common descent from a single 
recent ancestor (as in the HIV virus). These populations 
themselves fall into patterns, some being clearly similar 
and of the same species, others being different to varying 
degrees and thus of different species e.g. species of rats: 
Norway rat (Rattus norvegicus), roof rat (Rattus rattus); 
species of Prunus: plum, cherry, peach, apricot; species of 
large cats: lion, jaguar, leopard, tiger. Even though the 
exact definition of a species is a matter for debate, the 
species is used universally as the basic category of the 
classification. 
As the common names sometimes imply, some species 
are clearly members of recognizable larger aggregations (or 
the descendants of a common ancestral form) known as 
genera (singular, genus): e.g. date palm, canary date palm, 
dwarf date palm - species in the date palm genus Phoenix. 
This process of aggregating similar or related forms can be 
continued to form larger aggregations. Genera are 
aggregated into families, families into orders, and so on up 
the hierarchy as shown in Table 2.1-1. The higher 
categories of the hierarchy, such as families and orders, are 
vitally important for communication; they permit 
discussion, generalization and information retrieval about 
particular sets of organisms. The overall result is a 
hierarchical classification going the whole way from 
species (or even subspecies, or human-made varieties 
called cuitivars or breeds, within species) up to the major 
kingdoms such as plants, animals and fungi. 
To give some idea of our progress in understanding life 
on Earth a comprehensive, detailed classification of living 
organisms on earth compiled into a single work (Parker 
1982) recognizes 4 kingdoms, 64 phyla, 146 classes, 869 
orders and about 7000 families. However, recent advances 
in the study of cell organdies and DNA sequences have led 
to rapid changes in the topmost categories: Whittaker 
(1969) and Margulis and Schwartz (1982) propose five 
kingdoms and Woese (1994) places three domains above 
the kingdoms (as depicted in Figure 2.1-5). The total of 
1.75 million species thought to have been described to the 
present day represents a small fraction of the 13 to 14 
million species estimated to exist in total. There is at 
present no comprehensive catalogue even of these 1.75 
Characterization of Biodiversity 29 
(a) Rosaccac (Rose Family) 
Prunus Rubu 
Plum      Peach       Apricot Blackberry Raspberry 
(b) Rosaccac (Rose Family} 
Prunus Rubus 
Plum      Peach       Apricot Blackberry   Raspberry 
(c) Plum      Peach      Apricot Blackberry Raspberry 
Rosaceae (Rose Family) 
Figure 2.1-1: Three graphical representations of the laxonomic hierarchy of some members of the Rosaceae: (a) nested hierarchy; (b) 
box-within-box, and (c) a branching tree. 
million species (see Chapter 3.1 for further discussion and 
Tables 3.1.2-1 and 3.1.2-2 for species counts) 
Two properties of the taxonomic hierarchy are pivotal to 
its value in characterizing species diversity. First, the 
hierarchy provides a reference system that permits the 
summary, storage and retrieval of information about 
all organisms (Simpson 1961: Blackwelder 1967; Mayr 
1969; Farris 1979; Bisby 1984), Secondly, the hierarchy 
atletnpts to be natural, by reflecting the presumed pathway 
of evolution and the pattern of resemblances among 
the organisms (Darwin 1859; Haeckcl 1866; Cam 1954; 
Simpson 1961; Mayr 1963, Davis and Heywood 1963; 
Hennig 1966). 
2.1.0.! Folk classifications and the origin of scientific 
taxonomy 
Throughout history humans have classified organisms.  Wc 
use our innate classificatory abilities every day: we eat rice 
in quantity but not peppercorns. In supermarkets many 
foods are arranged by species. All human societies have 
folk taxonomies - traditional classifications of organisms 
often associated with cultural, survival and culinary 
practices (Berlin 1992). The limit of Fast Hudson Bay 
recognize two major kinds of animals, umajitq which are 
game animals, and umajuquts which are domestic ones 
(Atran 1990). The Tzeltal Indians of Chiapas, Mexico, use 
four life-forms - trees, herbs, grasses and vines (Table 2.1-2; 
Berlin el al. 1974), a system winch contains logical 
structures (generic tax a) analogous to the genus and species 
of scientific taxonomy. 
ft is from these folk classifications that scientific 
taxonomy emerged, initially in Europe, bringing together 
the more formalized cataloguing of medicinal herbs, world- 
wide collecting expeditions, particularly by the seafaring 
nations, and the dawn of scientific discovery in biology. 
Mediaeval herbals contained descriptions of herbal extracts 
JO Characterization oj Biodiversity 
Table 2.1-1: Major taxonomic categories. 
Categories (in descending rank} Examples 
Informal category above kingdom 
Domain Lucarya Eucarya Eucarya 
forma! categories recognized 
Kingdom* 
Phylum (Division)* 
Class (Super-, Sub-)* 
Order (Super-, Sub-)* 
Family (Super-, Sub-)* 
Tribe ( Super-, Sub-)* 
Genus (Super-, Sub-)* 
Section (Sub-)* 
Species (Super-, Sub-)* 
Variety (also Form) 
Cultivar Group, Cultivar 
Animal ia Planiae 
Chord ata Trac heo p h y ta 
Mammalia Angiospermae 
Primates Fabales 
Hominidae Legu mi n osae 
Hominini Vicieae 
Homo Pisttm 
Homo sapiens Pismn sativum 
P sativum var. sativum 
(Sugar Pea Groups cv. 'Olympia' 
Protect ista 
Ciliophora 
Oligohymenophora 
Hymenostomatida 
Parameciidae 
Parainecium 
Paramecium caudaium 
Further informal categories used 
Special form 
Pathovar 
Race 
Breed 
* These categories are often subdivided still further by the addition of the prefixes sub- or super- in addition to the stem ranks 
themselves, e.g. a superfamily may contain several families, and a family several subfamilies. 
Table 2.1-2; Folk taxonomy of the Tzeltal Indians of 
Chiapas, Mexico (from Berlin etal. 1974). 
Category 
fe^' trees' 
wamat 'herbs' 
?ak 'grasses' 
?ak 'vines' 
Unaffiliaied taxa 
Ambiguous taxa 
Total 
Number of generic taxa 
178 
1 19 
35 
:M 
97 
IB 
471 
and crude illustrations of the plants from which they came, 
often with a number of animal extracts and even inanimate 
items alongside. The thoughtless copying of such works 
and the attempts to shoe-horn into them new discoveries 
from all over the world soon led to chaos. It was against 
this background that the cataloguing energies of the 
eighteenth century Swedish naturalist Carl Linnaeus, and 
the first attempts at natural classification by the French 
naturalists, were so badly needed. 
For a long time species were named using a descriptive 
Latin phrase, but no formal system was widespread. It was 
Linnaeus who adopted the binomial system in later editions 
of his master catalogues Systema Naturae (Linnaeus 1735) 
and Species Plamarum (Linnaeus 1753), and a system of 
nomenclature broadly similar to his has continued to the 
present day. It is now formally embodied in the various 
Characterization of Biodiversity 
Table 2.1-3: The Codes and Committees dial define rules and recommendations for the scientific names oftaxa. 
31 
Relevant publication or authority Abbreviation Latest edition 
iCZN ICZN 1985 
iCBN Greuter et at. 1994 
1CNB Sneath 1992 
1CTV Frankiefo/ 1990; Mayo 1994 
ICNCP Brickcll et ai. 1980 
International Code of Zoological Nomenclature 
International Code of Botanical Nomenclature1 
international Code of Nomenclature of Bacteria1^ 
International Committee on the Taxonomy of Viruses 
International Code of Nomenclature of Cultivated Plants 
1. Blue-green algae (Cyanobacteria) have variously been treated as plants or bacteria, giving rise to confusing applications of both 
ICBN and ICNB. 
2 Fungi are covered by the ICBN/as are Cyanobacteria and certain Protozoa. 
international rules for nomenclature and almost universally 
endorsed as the scientific names of organisms. Starting in 
the same period, much of the classification that we use 
today was put in place by de Jussieu, Adanson, Cuvier, 
Lamarck and Geoffroy Saint-Hilaire. It was they who 
recognized the major natural groupings of animals and 
plants, albeit without Darwin's insights into evolution or 
today's understanding of phylogenetic taxonomy. The 
classification and nomenclature system has developed 
continuously from that time and now enables workers in all 
sorts of professions from all over the world to communicate 
reasonably effectively about the same organisms, be they 
plants, animals, fungi or other microorganisms. 
2.1.1 The basics of taxonomic characterization: what 
taxonomists do 
There are common elements to nearly all taxonomic studies 
despite the different practices relevant to different groups 
of organisms (Blackwelder 1967; Davis and Heywood 
1963). Most studies start from the examination of live or 
preserved specimens, either because newly discovered 
specimens do not fit the known patterns, or because 
specimens are being re-examined to solve a problem in the 
existing taxonomy. Some specimens are found to belong to 
already-known species. They are identified and the data 
associated with the specimen are added to the 
documentation for the species, possibly adding new 
localities, or variations in the description Others prove to 
be of a previously unnamed organism. After careful 
research in the literature, and thorough examination of the 
new taxon, a new species, subspecies or variety is 
described and named using the international codes of 
nomenclature (see Table 2.1-3). 
Ideally most taxonomic studies would be revisions of an 
entire group of organisms over its complete geographical 
range - a whole genus, family or order - but this is difficult 
to achieve both because of the labour involved and because 
of the logistics needed to see specimens or cultures and 
study the organisms over several continents. Depending on 
the size of the group and its distribution, it may take 
anything from three to ten years of full-time work, in 
extreme cases even a lifetime, for a taxonomist to complete. 
The advantage is that all species can be examined in a 
comparable way, and that if all have been examined, 
decisions and descriptions of genera and families will not be 
confounded by intermediate or more extreme species missed 
out of the study. Such studies involve examining all 
available specimens, often by loans from the major 
collections supplemented by local and specialist collections, 
followed by the publication of a clear summary of the taxa. 
It is also important to ascertain the correct name for each 
taxon plus synonyms where they occur. 
2.1.1.1 The role of specimens in taxonomy 
Collections of biological specimens serve several distinct 
fundamental functions in the characterization of 
biodiversity. One of these, discussed here, is as the raw 
material for taxonomy: all taxonomic research is based on 
the comparison of large numbers of specimens. Equally 
important for biodiversity survey and inventory is the use 
of these same collections of specimens as the raw data for 
biological recording, discussed in Section 7: the time, the 
place, and the species for each biodiversity data point come 
from one of these specimens. We thus think of the 
collections of living and preserved specimens as 
fundamental resources for biodiversity assessment world- 
wide, the subject of Chapter 3.2. A third, specialist, usage 
is for so-called type specimens used to fix the application of 
names to organisms, discussed in 2.1.1,2 
The specimens needed by taxonomists cover a very wide 
range: preserved specimens in museums and herbaria, 
living specimens in zoos, aquaria, botanic gardens, 
arboreta, germplasm banks and culture collections; and 
associated data such as descriptions, illustrations, chemical 
32 
(a) 
Characterization of Biodiversity ': 
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cccccTC'reiG--cc,ri'AATrcG,i'ctx:cccecw:ATCcccc"i,i:'A,rriiAC'i,c 
Tl' AT A' l" I -] TGC TC A1 - PC ATI "IV! C r AC I 'A i ? A AC A] -1 TrCCT C AT i'T AC TC 
CiCATCCCTCC- - C AT PC AKTlt"! CGCCT AIXJOl ATC C I CC;T(. A" T r ACTt! 
Figure 2.1-2: Comparative data in systematics: (a) gross morphological features in pine trees (Pinus, Morin el al. 1993), (b) microscopic 
features of gcnitalia in bumble bees {Bombus, Alford 1975), (c) oscillograms of grasshopper calling songs (Enckortkippus, Raggeand 
Reynolds 1984), and ((/) 18S ribosomal DNA sequences (from the V4 hypervariablc region) in flagellates (Paraphyso/nonas imperforata, 
P. butcheri, P. vestita and P.foraminifera, Accession Nos. Z29680, 229679, Z28335 & 233646 in the EMBL Sequence Data Library, 
communicated by J Rice, 1995). 
records, sound recordings and genome sequences stored in 
libraries, film and tape archives and computer databases. 
There is a need to marshal large numbers of specimens 
from the full geographical range side by side for 
comparison, and to document and preserve evidence of 
diversity with specimens providing fixed data points. 
Taxonomists need to see the widest possible range of 
specimens for the group of organisms under study. A full 
geographical and ecological range, plus specimens of 
differing life stages and temporal variations are needed: 
juveniles and adults, vegetative and reproductive, male and 
female, winter and summer plumage, larvae, pupae and 
adults, seeds, eggs or spores as appropriate to the organism. 
The specimens used for accessing these vary from entire 
populations {e.g. a bacterial culture), to individual plants or 
animals (eg. a pressed plant or a pinned insect), to 
fragments such as fruits, skulls, skins or blood samples. 
Associated data sets such as DNA sequences, oscillograms 
of animal calls and behavioural recordings may be relevant 
too. Some different data types are illustrated in Figure 2.1-2. 
Ideally the data used for studying each group of 
organisms will span an immense range of characteristics 
drawn from different organs, different life stages and 
different aspects of the biology (sec Figure 2.1-2). It is the 
morphology (physical shape and structure of the organism) 
and the anatomy (shape and structure of internal organs) 
that are most easily available and consequently most 
widely used. Even microscopic details, e.g. of insect 
genitalia or of fungal spore sculpturing, are often well 
preserved. Modern techniques such as electron microscopy, 
phytochemical analyses and DNA sequencing can often be 
applied to specimens of all ages, 
Taxonomic research increasingly involves substantial 
work in the field to study the living organism in situ, or to 
establish living collections in a laboratory setting. This is 
an opportunity to collect data that cannot be obtained from 
preserved specimens, such as physiological measurements. 
Behaviours such as feeding or food plant preferences, 
locomotory patterns, mierohabitat preferences, timing of 
sexual or other biological activity (phenology, diurnality 
Characterization of Biodiversity i.< 
versus nocturnality, migration, circadian rhythms in depth 
for oceanic plankton), can all contribute to a systematic 
study Many species build burrows, nests, brood chambers. 
retreats, webs, moulting chambers, egg-sacs, and other such 
constructs. Where these behaviours reflect heritable 
variation they provide valuable sources of systematic data 
revealing patterns of variation comparable to those in 
morphology and anatomy. Samples destined for gene 
sequencing, particular forms of anatomical comparison, or 
chemical analysis may require special techniques of 
preservation. Videotapes of behaviour or audiotapes of 
calls are obtainable only through fieldwork and must be 
stored and preserved in special repositories. 
Each specimen collected in the field and deposited in one 
of the public collections is of potential value far beyond the 
particular study or programme for which it was collected. 
There is a consequent responsibility on the collector to 
establish without doubt the minimum parameters: location 
(increasingly giving precise latitude and longitude using a 
global positioning device), altitude or depth, date of 
collection and an identifying unique collector's name and 
number. Other valuable data are items that cannot be 
derived from the specimen at a later date - such as 
substrate, odour, sounds, colours (which often fade), 
behaviours, and position on a host. Maximum benefit will 
be obtained if, possibly after immediate usages, every 
specimen is deposited in a public collection where it can be 
used many times to contribute to biodiversity knowledge: 
the resources thus generated are reviewed in Chapter 3.2. 
For the system of specimen usage to work well amongst 
taxonomists it is important that at least one duplicate of 
each specimen, or the single specimen itself, be deposited 
at a public collection in the country of origin (this is 
usually a condition of collecting permits), and that such 
collections should make the specimens available for loan to 
taxonomists. 
2.1.12 Stability of scientific names 
The object of scientific nomenclature is to provide a stable 
unique name for each organism (.Jeffrey 1989}. The usage 
and giving of names is governed by the various 
international codes of nomenclature winch, for historical 
and biological reasons, are slightly different for certain 
major groups of organisms (Table 2.1-3). All of the codes 
provide a mechanism for publishing a new name for a 
newly recognized taxon. for fixing a name to a particular 
organism by citing a type, and for arbitrating between 
synonyms where a taxon has accidemly been named more 
than once, or where two tax a have been united into one. 
he type of a species name is a particular cited specimen in 
a particular collection, the type specimen. The continued 
preservation of type specimens in public collections is 
important so that subsequent checks can be made that the 
ri?nt name is being applied to the right organism. 
In many cases the giving of names has proved to be a 
troublesome business (QuickC 1993). On the one hand it is 
essential that taxonomists continue [o map the pattern of 
variation and descent: this leads to changes in the 
classification and consequent changes of names, an 
inevitable price to pay for progress. We do need these 
changes if modern data and new discoveries are lo be 
incorporated into our view of the taxonomy. More 
troubling, however, are cases of seemingly unnecessary 
name changes arising from different interpretations of the 
rules, or the continual discovery of older names that take 
priority under some of the codes Recent discussions have 
started a move to climinale such nomenclatura! changes, 
either by permitting certain names to be conserved, or by 
listing names In current usage and protecting them from the 
priority of older names (Mawkswonh 1991, 1992) 
Some problems arise from the existence of different 
codes for different groups of organisms. Certain organisms, 
such as the blue-green algae, have even been treated 
variably under one code or another, leading to ambiguity or 
duplication (Table 2.1-3). There are also cases of 
organisms under different codes being given the same 
name: the names must be unique but only within the 
domain of one code. Steps are being taken to harmonize the 
existing codes and a working body of TUBS is now 
discussing the difficult task of preparing a unified code for 
all organisms (Hawksworth 1994; Hawksworth et at. 1994), 
Common or vernacular names, although often used very 
precisely in a given community, are usually neither unique 
nor universal. The problem is a tendency to re-use common 
names for wholly or slightly different organisms as human 
communities, colonial powers and languages have moved 
from one place to another. The names vaeiam and retama. 
for instance, cover a wide range of plant species in Arabic-, 
Spanish- and Portuguese-speaking countries. 
2,1.2 Characterizing flora, fauna and microhiota: 
preparing Floras, handbooks and keys 
One of the main tasks of taxonomy is to characterize the 
species of plants, animals and microorganisms so that they 
can be recognized, used and studied by others. With the 
exception of the orally communicated folk taxonomies IA 
indigenous peoples, biologists all over the world have. 
since the eighteenth century, drawn their knowledge on 
species characterization from the primary catalogues 
created by the lie Id work and research of an international 
community of taxonomists. Ke> elements in these primarj 
works are (I) the classification twhat species and higher 
laxa exist). (2) the nomenclature (unique scientific names 
for the species and higher taxaj. (3) descriptions of the 
organisms in these species and higher taxa. and t4; 
identification aids (with which to identify to winch species 
and higher taxon a freshly encountered specimen belongs I. 
Linnaeus called his primary catalogue a Systema Naturae 
34 Characterization of Biodiversity 
(Linnaeus 1753) and recent electronic publications use 
phrases such as Species Diversity Information System (e.g. 
the 1LDIS LegumeLine database, Zarucchi et al. 1994; 
Bisby et at. 1994) and Expert Identification Systems {e.g. 
the ET1 CD-ROM Linnaeus Protist, Lobsters of the World, 
Estep et al. 1992: Estep and Rey 1993: Holthius 1994): but 
the majority are published books called Floras. Faunas, 
Monographs, Catalogues, Checklists, Handbooks or Keys. 
Vascular plant primary catalogues fall into two classes: 
Floras and monographs. Floras document all of the higher 
plants in a given land area, such as local Floras, national 
Floras and regional Floras. National Floras exist for quite a 
large set of nations (see Frodin (1984) for coverage) and 
regional Floras have been completed for the former USSR 
(Komarov et al. 1934-60), for Europe (Tulm et at. 
1964-80) and for West Tropical Africa (Hutchinson and 
Dalziel 1927-36). Projects are in progress for some other 
regions (e.g. Flora of North America. Morin 1993 et seq.; 
Flora Matesiana, van Steenis 1948 et seq.) but for many 
species-rich tropical areas there is still no effective 
inventory. Botanical monographs document all plants in a 
given higher taxon world-wide or in a region, as in generic 
and family monographs 
In practice the study of a major taxon world-wide is 
often not practicable, so there are few worldwide 
monographs, mostly of genera, and rather more regional 
monographs of genera or families. Again, there are no 
recent monographs of the large or tropical plant families. 
For animals, the pattern is much less tidy, and for good 
reason1 The equivalent to the plant scene would be Faunas 
(all animals of an area) and monographs (all animals in a 
group, world-wide). But there are so many more animal 
species, and they belong to widely different groups, each of 
which may have its own discipline of specialists, such as 
entomologists, herpetologtsts, ornithologists, lepidopterists, 
etc. Most descriptive works are restricted to a single higher 
taxon and are variously local, national or occasionally 
regional in scope. The result is an even more patchy 
coverage than is found in plants with not only some 
overlaps, but very, very large gaps: many major groups are 
uncatalogued for large parts of the world. Even the best- 
covered countries (in Western Europe and North America) 
have far from complete coverage of all animal groups 
Standing way above the other problems is the difficulty in 
cataloguing insects (over 950 000 world-wide Wilson 
1992), of which the beetles, Coleoptera, dominate with 
290 000 species. Where Fauna projects have been 
undertaken, as in the Faune de France (FFSSN 1921-66), 
the work is always segmented into different volumes 
researched by different authors. There are rather few 
guides to the coverage of the world's animals: notable are 
Sims and Hollis (1980). Animal Identification in three 
volumes covering marine and brackish water animals 
(Vol. I), land and freshwater animals excluding insects 
(Vol. 2) and insects (Vol.  3), and Key Works for 
Northwestern Europe (Sims et al. 1988). 
Lastly - what is the level of treatment of the other major 
groups, such as marine and lower plants, marine animals, 
fungi, bacteria and the viruses? There are some groups that 
are partially covered: the bryophytes, mosses and 
liverworts (rather few species and reasonably accessible to 
field botanists), fish (of economic importance), some 
bacteria (of medical importance) and some fungal groups 
(of economic importance). For most of the rest, coverage is 
sparse indeed: few coherent catalogues exist even for the 
many species known to taxonomists, let alone the vast 
numbers of species yet to be discovered. 
2.1.2.1 The amount of research work involved 
The type and amount of research needed to create one of 
these primary works varies enormously, particularly with 
how many species are to be covered, whether the group of 
organisms is well or poorly known, and how well explored 
is the region to be covered. For poorly-known groups and 
little-explored areas, years of field exploration may be 
needed both to accumulate sufficient specimens of each 
species encountered and to increase the chances that all 
species in the area have been encountered. Conversely, for 
well-known groups and much- explored areas there may 
already be a plethora of material lodged in museums or 
herbaria: die problems relate more to seeing all this material 
(borrowing it or visiting it), and to sorting out conflicts in 
existing taxonomic treatments of the organisms. Depending 
on how full a treatment is prepared, and particularly on 
whether all four elements are represented (classification, 
nomenclature, description and keys), the creator of the work 
will need to pass the following milestones: 
1. Form a concept of the exact set of species being treated, 
often involving decisions on: 
? what are the species: how are they delimited, how are 
problems of apparent overlap, intermediacy, 
hybridization and discontinuity dealt with; 
? how are these species classified, either within the 
existing published classification, by extending the 
classification, by adjudicating between alternative 
views, or by creating a new classification 
2. Form an opinion on the correct (or new) name for 
each species and each higher taxon, and on the names 
and taxa from other treatments to be placed in 
synonymy. 
3. Create a description of each species by studying the 
range of variation within that species as evidenced by 
field observations or by examining preserved specimens. 
The range of variability in one area may be greater or 
Characterization of Biodiversity 
Fieure 2.1-3: {a) Annual rales of production of" trie major regional Floras (Polhill 1990). 
J5 
Flora Started First Species Total % Species/ Actual or projected 
issue published year completion 
Europaca 195% 1964 11 557 - 100 770 1978 
SSR 1931 1933 17 520 - 100 515 1964 
Australia 197V 1981 2 631 18000 15 329 2043 
West Tropical Africa 1951 1954 7 349 - 100 387 1972 
Neotropica 196% 1968 4 624 90 000 5 220 2397 
Southern Africa 1966 2 834 19 500 15 17.1 2124 
Zambesiaca 1956 1960 3215 9 300 35 110 2044 
Tropical East Africa 1949 1952 6 425 10 500 61 173 2013 
Malesiana 1947 1954 4 837 25 000 19 1 IS 2135 
(b) Total number of species treatments published in major regional Floras, in five-year intervals (Polhill 1990). 
iKXn 
o 
' ??-> 
Sftl 
-:>:: 
? 
B 
200 
I970-75 
less than that recorded in other works for other areas. 
Additional descriptive features such as illustrations, 
distribution maps, ecological features, etc. may be added 
as well. 
4. Create an identification key that leads unambiguously to 
an identification for freshly encountered specimens. 
Where possible easily visible, clearly demarcated 
characters should be used. 
To give some idea of the amount of work involved, we 
cue the successful completion of Flora Europaea (Tutin et 
at. I 964?a0). [is five volumes, containing a medium 
(synoptic) rather than full treatment of 11 557 plant species 
from the well-known, well-collected flora of Europe took 25 
years work for a network of full- and part-time specialists 
to complete. But progress is much slower in the 
tropical regional Floras where more original research and 
ficldwork is needed, as illustrated in Polhill's (1990) 
comparison of nine regional Floras summarized in Figure 
2-1-3 a and 6. 
Floras. Faunas, monographs, many handbooks, and guides all 
tend to contain all four elements - classification, nomenclature, 
descriptions and keys. However, there can be substantial 
variations in how complete the descriptions are, whether 
voucher specimens are cited, whether illustrations and maps arc 
included and in the extent of additional ecological, behavioural 
or economic ml on nation given ('heck lists normally contain I he 
classification and nomenclature of species, but accompanied by 
just a geographical distribution - no descriptions or 
identification aids, They are produced either as quicker projects, 
or to cover a wider geographical or taxonomic range than could 
otherwise be contemplated for full treatment. Keys are 
sometimes published atone, as a preliminary to fuller treatment, 
as companions to existing works, or to resolve urgent needs lor 
identification in economic or medical contexts. 
2.1.2.2 Modern developments: databases and expert 
identification systems 
This is written at a time of unprecedented change in the 
technology and dissemination of primary and other 
taxonomic works. Information technology is rapidly 
36 Characterization of Biodiversity 
bringing in electronic communication amongst dispersed 
taxonomic contributors working as teams, the creation of 
major taxonomic works as databases, and the electronic 
dissemination of information to users by communications 
networks such as Internet or hy CD-ROM disks. Some of 
the electronic products are simply electronic versions or 
compilations from existing primary works, but increasingly 
major primary projects are being compiled in this way: for 
instance the ICLARM/FAO bishBase international project 
on fish (Lourdes et at. 1994: Froese and Pauly 1994) 
incorporates the primary database on fish genera and 
species (rischmeyer 1990. 1992). and the ILDIS species 
diversity system on legume plants is based on a fresh 
synthesis of the species taxonomy of Lcguminosae by a 
world-wide network of experts (Zarucchi et al. 1994; Bisby 
et at. 1994). 
A particularly important development is the bringing 
together of two technologies, the use of descriptive data 
tables in computer identification routines (Pankhurst 1975, 
1978, 1991; Dal I wit? 1974. 1980). and the facilities in 
modern computing environments to use windows 
containing diagrams, illustrations, photographs and maps 
The resulting expert identification systems such as those 
produced by the Dallwitz school using the DELTA format 
(Beetle Larvae of the World, Lawrence et al. 1994; 
Families of Flowering Plants, Watson and Dallwitz 1994) 
and by ETI, the Expert Centre for Taxonomic Identification 
(Linnaeus Protist. Estep and Ray 1993; Lobsters of (he 
World. Hohhius 1994) are surely the sign of things to come. 
Electronic means are also opening up the possibility of 
creating master catalogues both of larger and larger groups, 
and eventually of all known organisms. The IOPI World 
Plant Checklist (Burnett 1993; Bisby et al. 1993) and the 
BIOTA Terrestrial Arthropods projects (Hodges and 
Thompson, in press), for instance, propose to list all plants 
and all terrestrial arthropods. Very many groups of 
organisms now have rapidly progressing master catalogue 
systems (Bisby 1993. 1994) and the Species 2000 program 
of IUBS. CODATA and 1UMS is proposing that many of 
these create a federated system which could lead to an 
index of all of the world's known organisms 
2.1.3 Characterizing systematic patterns: the species, 
their evolution and their classification 
With the publication of Darwin's On the Origin of Species... 
in 1859. a major change was initiated in the way that the 
hierarchy of life was understood. Darwin's theory of 
evolution made sense of the natural patterns observed in the 
variation between organisms. Evolution occurs when 
organisms experience genetic mutations or recombinations. 
or when gene frequencies in populations change because of 
differing rates of reproduction or mortality Through 
natural selection or genetic drift these heritable changes 
may spread throughout the population and over time can 
lead to the production of new lineages closely similar to 
their relatives but differing by the possession of one or 
more new features (Ridley 1985, 1993; Futuyma 1987; 
Skellon 1993). If this new lineage continues to diversify 
throughout evolutionary time-spans, a wholly new higher 
laxon (lineage or clade) comes into being. Such lineage 
diversification produces a strictly hierarchical pattern. The 
roughly 4.5 billion years of biotie evolution has led to an 
enormous diversity of living forms on Earth. These forms 
can be grouped as sets within sets (a nested, hierarchical 
pattern) based on how recently they shared a common 
ancestor. 
Darwin's observations of selective breeding and the way 
In which characteristics could he inherited, coupled with 
the immense diversity of different forms, for example of 
the birds and reptiles lit; sa? on Ins voyage ;u tin- 
Galapagos, suggested to him that heritable differences 
between individuals could build up to produce new species 
and consequently higher taxa over long periods of time. 
Darwin himself was unaware of the mechanisms of 
genetics, but later studies have revealed how characters are 
heritable and mutable. Genetic mutation and recombination 
can each produce heritable novel characters which either by 
the process of natural selection or by non-selected random 
genetic drift lead to populations in different places 
diverging from one another over time (refer to Chapters 4.2 
and 4.3). 
Thus the products of evolution are arrayed in natural 
groups which all people, to a greater or lesser extent, can 
recognize. The evolutionary explanation of this pattern and 
diversity is the most important rationale for the taxonomic 
system used by scientists. This arrangement of the diversity 
of forms of organisms into a hierarchy serves our goals of 
communication, and information storage and retrieval, by 
reflecting the evolutionary process that created these forms 
in the first place. 
2.1.3.1  Analysing systematic data to reconstruct 
evolutionary history 
The results of the evolutionary process described above can 
be reconstructed by careful comparative study of the taxa 
involved (Hennig 1966; Eldredge and Cracraft 1980; Wiley 
1981; Crisc 1983; Forey et al. 1992). Evolutionary 
mutation results in one of three patterns; new features arise, 
old features are lost, or pre-existing features are 
transformed to a greater or lesser extent. Any of these 
patterns are evolutionary changes In practice, taxonomies 
find such heritable changes at all levels of the taxonomic 
hierarchy and at all levels of organ is imc organization, from 
single changes in DNA sequences to large changes in 
skeletal organization or even the entire body plan of 
the organism. 
Because descendants inherit the features ot their 
ancestors, a new mutation that first appeared in the ancestor 
| 
I 
Characterization of Biodiversity 
nds to be passed to its descendants. The set of all 
organisms, living and dead, that descended from thai 
original modified ancestor is known as a lineage or clade 
The novel mutation is known as a character, trait or feature. 
The old version of the trait is termed primitive, and the new 
version is derived. Over immense spans of geological time, 
speciation may occur so that the lineage splits into several 
to many species. Subsequently mutations may occur that 
delimit subsidiary lineages. From a strictly taxonomic point 
of view, why these changes occur, or whether they are 
beneficial, neutral or even detrimental to the species in 
which they occurred is irrelevant. What matters is that any 
given group of taxa both agree and differ in which 
characters they possess. Thus spiders are the only 
Arachnids that have terminal abdominal spinnerets and 
thoracic poison glands that open through the fang. On the 
other hand, only some spiders can make viscid, sticky silk; 
the webs of other species are dry. The simplest hypothesis 
is that the common ancestor of all spiders had spinnerets 
and fangs, but that only the common ancestor of a 
particular subset of spiders made viscid silk. For this 
simple case it is easy to see how important events in 
evolutionary history are reconstructed. The evolution of 
poison fangs and spinnerets marks the origin of spiders, 
and the invention of viscid silk marks the origin of a 
particular subfamily of spiders, the Araneoidca, 
In evolutionary theory, characters of organisms that are 
similar because of inheritance from a common ancestor are 
called homologies. Classic examples are the wings or 
feathers of birds. No other group has feathers, and close 
examination of any feather discloses additional complex 
similarities that substantiate the homology of feathers. 
Another example is the sting of a wasp, actually the 
modified female ovipositor. Only some Hymenopteran 
species have stings, and in all of these species the sting is 
always the modified female ovipositor. 
If evolution consisted only of the gain of complex 
homologies that were never lost by descendants, 
reconstructing evolutionary history would be simple indeed. 
Two processes complicate the issue. First, natural selection 
is amazingly efficient at moulding what appears to be the 
same feature from different starting points, a phenomenon 
termed evolutionary convergence. The wings of birds and 
bats are so similar that many years ago the homology of the 
two features was an open question. Detailed comparison, 
however, revealed substantial differences The.fleshy, spiny 
stems of some African Euphorbia plants are convergent on 
those of New World cacti. Porpoises are mammals, not fish, 
despite their fins. However, often the only way to test if two 
features are convergent or truly homologous is through 
quantitative analysis. 
The second process that complicates systematic analysis is 
loss of features. Snakes originally had two pairs of limbs like 
other terrestrial vertebrates, but most have lost all trace of 
,o 
37 
Character 1 
Character 2 
Character 3 
Character 4 
Character 5 
Character 6 
Character 7 
4   0 
t j j 
i % 
Cow 0 0 1 1 0 0 0 
Horse 0 0 1 i 0 0 0 
Cat 1 0 0 0 ] 1 1 
Fox 0 I 0 0 1 I 1 
Wolf 1 1 0 () ]. 1 1 
Figure 2.1-4: A simple data matrix and the implied phylogenetic 
hypothesis of four taxonomic groups. 
them. Fleas may not have wings, but many other features 
betray their relation to winged insects. Once again, it is 
frequently impossible to distinguish secondary loss of features 
from primitive absence except through quantitative analysis. 
In practice, systematic data are compiled as a matrix of 
characters by taxa and analysed quantitatively by computer. 
By reading across (or down) the matrix, one can either read 
off all the relevant characters of a particular taxon, or 
conversely see which of a number of taxa possess a 
particular feature. The computer analysis is designed to 
provide the best possible estimate of the phylogeny of the 
group (as described above), expressed as a branching 
diagram or evolutionary tree. Such diagrams are often 
called trees, phylograms. dendrograms, or cladograms 
(because they indicare relationships between clades of 
organisms). For simple examples of straightforward data, 
the best estimate of the phylogeny is often obvious (Figure 
2,1-4). but for larger numbers of taxa and characters, 
computer algorithms are used to produce estimates 
(Kitching 1992). A number of different algorithms ate 
currently available (e.g. parsimony, maximum likelihood, 
or neighbour-joining techniques), and the subject ol 
which provides the best estimate under what circumstances 
is an area of very active research (Swofford and Olsen 
1990), 
38 Characterization of Biodive rsity 
Box 2.1-2:  The relationships of the cow, horse, cat, 
ox and wolf. 
Cow Horse Wolf 
For this tree the groups are: 
fr 
Cow 
^= 
Horse 
(r        -<s   ( \ (  
Cat           Fox      Wolf 
\s-?J)   ^ /\  
and these groups can be convened to taxa in the 
laxonomic hierarchy: 
fcow) (Horse]    (^Cat ")   ( Fox ] (wdfj Genera 
(cowj (Horse]    fcat~]    Fox Wolf     Subfamilies 
Cow      Horse Cat       Fox       Wolf Families 
2.13.2 From phylogcnestc trees to format classifications 
The trees that result from comparing characters in species are 
usually thought to be a graphic representation of the 
evolutionary relatedness of the taxa. These trees should be 
viewed as relative statements of relationship. For example, in 
Box 2.1-2 the wolf and the fox are hypothesized to share a 
more recent common ancestor with one another than with the 
cat, but the cat, wolf and fox all share a more recent common 
ancestor with one another than with I he hoofed mammals such 
as cow and horse: the tree, therefore, shows a hierarchy of 
relationships. A tree does not explicitly hypothesize 
ancestor-descendam relationships. For example, the tree 
hypothesizes that wolf and fox are related, but not that 
wolves evolved from foxes or that foxes evolved from wolves. 
One of the tasks of a taxonomist is to convert this 
graphic representation ol relationship into the formal 
hierarchical classification of taxonomic categories such as 
genus, family, order, etc. In converting the tree to a 
classification, the systcmatist gives groups that share a 
common ancestor the formal taxonomic names Such 
groups are called monophyleiic taxa and they are 
recognized because they share unique derived characters. 
The tree shows several sets of most closely related taxa that 
are nested within larger sets thai contain additional taxa. 
These larger groups are, in turn, nested within even larger 
groups By this process the phylogenetic tree is 
transformed into the taxonomic hierarchy used as a 
classification. In creating categories, systematise choose 
sets that naturally reflect the hierarchy inherent in the tree. 
Despite the utility of the traditional taxonomic hierarchy 
in summarizing diversity and evolutionary relatedness, 
there are real problems in incorporating elements of the 
phylogeny into the hierarchy in a precise way. The 
difficulties relate to the subjectivity in deciding taxonomic 
rank, and the fact that phylogenies often imply hierarchies 
with more levels and greater asymmetry than is allowed in 
the taxonomic hierarchy. A simple example given in Box 
2.1-3 makes this clear. 
Some biologists (lumpers) stress similarities held in 
common by the organisms being studied and so tend to 
group several species into a single genus as in Box 2 1 -3 (a). 
Others (splitters) stress differences between the species and 
so tend to divide the species into several different genera 
(Corliss 1976) as in Box 2.1-3 (rf). 
As a group of species is studied in more detail, it is not 
uncommon for it to be ever more finely subdivided or for 
the group as a whole to be elevated to a higher taxonomic 
category. This simply reflects the fact that detailed study 
uncovers more characters that emphasize the differences 
among the species, Microsporidia, which comprise a 
unique group of obligate, intracellular parasitic protists, are 
such a group now receiving increased taxonomic attention. 
Until recently, their ubiquity did not cause a threat to 
humans and few systematists worked to describe and 
classify the species. But since 1985, physicians have ? 
documented an unusual rise in worldwide infections in 
AIDS patients caused by four genera (Encephalitozoon, 
Nosema, Pleisiophora and Enterocytozoon), and 
identifying microsporidian species is impeding diagnosis 
and effective treatment of patients. As a result, research has 
been focused on the group and the number and diversity ot 
forms observed have risen sharply. 
2.1.3.3 Why do classification schemes change? 
Scientists working in genetic resources, biotechnology, 
agriculture, conservation and other disciplines that use 
existing classifications are often disconcerted to find that 
systematists change the classification scheme. These 
changes are, however, just the logical consequences of 
discovery of new data and new taxa, and correction of two 
kinds of mistaken interpretation. 
New technologies constantly give rise to new sources of 
character information. New information reveals new 
similarities and differences among taxa that cause us to 
revise the placement of a tax on in a tree, or to choose to 
Characterization of Biodiversity 
.W 
Box 2.1-3: A phyloficnetic tree which shows relative reialcdness between len species (A-J). 
AGCDEFGHI 
In this tree, A and B share a common ancestor and so are called sister taxa. Examining this tree you see that D and 
E, F and G, and I and J are also sister taxa. The sister group to species C is the group A + B, and so forth. There are 
several different ways to sort these species into acceptable, monophyletic genera, shown below. For example, the 
decision to place taxon C as one of many species in a genus {a) or as a single species in its own genus (d) is an 
artificial decision based on the personal preference of the taxonomist. 
(h) 
id) 
lump or split a taxon within an existing classification. An 
example of this sort of change is illustrated dramatically by 
the revision of prokaryote classifications resulting from 
molecular genetic data that have become available only 
within the past decade (Figure 2. 1 -5 ). 
The discovery of previously unknown species will also 
change classifications. If unique, these species will have to 
have new taxa created for them. In addition, they have new 
characters or new combinations of characters whose study 
revises our hypotheses about evolutionary relationships of 
a|l the taxa. There have been some recent spectacular 
discoveries of new vertebrates such as the plankton-feeding 
megamouth shark described in 1983, the Vu Quang 
antelope of Southeast Asia in 1993, and the golden bamboo 
?emur (Hapalemur aureus) from Madagascar in 1986. Bui 
llus is only lite lip uf the ia-bcr';.1. Many more new -,pivu\ 
(especially microscopic organisms) are waiting to be 
discovered. Indeed, we cannot presently say how many 
species exist on Earth and some people's estimates range 
over an order of magnitude, from 5 to 80 million species. 
For most species thai have been documented, relatively 
little is known about their historical relationships. 
biological characteristics, or distributions within the Earth's 
habitats and ecosystems 
The first common sort of interpretative mistake that 
bedevils systematic analysis is the discovery thai the 
defining features of a taxon are convergent rather than 
homologous (see 2 I 3.1). The taxon then is known to be 
polyphyletic (the taxa do not share a recent common 
ancestor but instead the group has been defined by a 
40 Characterization of Biodiversity 
Animal!,! 
Antmaltb 
(C) 
Bacteria Archaea Eucarya 
T isc -noi&3ai*s  
Figure 2.1-5: Fundamentally fifferem views of the taxonomy of 
life based on [a] gross morphology (two kingdoms as 
re con st rue led by Whitlaker 1969), (h) cell structure and organdies 
(five kingdoms, Whittaker 1969) and (c) DNA sequence data 
(three domains, Woese 1994). 
superficial similarity that does not indicate evolutionary 
relatednes.s). When this happens, the polyphylclic groups 
arc abandoned and several monophyletic taxa are created in 
its place. For example, in Figure 2.1-4. the evidence of 
character 1 conflicts with thai of 2 and 3. Either characters 
2 and 3 are homologous and I is convergent, or the reverse. If 
scientists did not know of characters 2 and 3, but only of I and 
4-7, the evidence of character 1 would group the cat with the 
wolf to the exclusion of the fox. Hence discovery of characters 
distributed as 2 and 3 can change phylogenetic hypotheses. 
In practice, most systematise do not change official 
classifications until the new results have been corroborated 
and widely accepted, bui the pace of taxonomic discovery 
is so fast thai classificatory change is still rather frequent. A 
real example is the almost complete restructuring of 
bacterial classification in the last 15 years (Figure 2.1-5). 
The second common error found in taxonomic 
classifications occurs because primitive features of 
organisms have been mistakenly interpreted as novelties, or 
derived features, and used to define a group (see 2.1.3.1), 
In Figure 2.1-4, the cow, horse and cat are alike in 
characters 2 and 3. However, grouping these three taxa on 
the basis of characters 2 and 3 would be incorrect because 
they share no unique common ancestor. The only ancestor 
that includes cows, horses, and cats also includes foxes and 
wolves. The implication is that any biological prediction 
made for cows, horses and cats will either be true also for 
foxes and wolves (if it evolved at node 1, Figure 2,1-4), or 
for an even more inclusive group of mammals (if it evolved 
prior to node I). Groups defined by primitive features are 
called paraphyletic because they include only some of the 
descendants' most recent common ancestors. For example, 
scientists used to call all animals except vertebrates the 
Invertebrata. But the only defining trait of invertebrates is 
the absence of a vertebral column, an absence equally well 
shared with tomatoes and, for that matter, stones Aside 
from the original observation (that some species lack 
vertebrae), invertebrates as a group share no traits not also 
present in at least some vertebrates. 
2.1.4 Characterizing species 
For as long as humans have observed the tremendous 
diversity of life, they have attempted to sort organisms into 
recognizable kinds and to give names to them. In all groups 
of organisms the basic unit of classification is the species. 
The earlier concept of fixed and unchangeable kinds can be 
traced to the idealism of Plato and Aristotle. Belief in the 
notion of fixity continued to influence biology into the 
tiinteenth century until destroyed by evolutionary thinking. 
Today, species arc recognised and conceptualized in 
three rather different ways. They may be seen to be distinct 
(the morphological species concept); members of the 
species may be united by shared inheritance from common 
ancestry (the phyiogenetic species concept); and there may 
SM1 '' 
Characterization of Biodiversity 
be biological processes such as mating, recognition and 
behaviour thai unite members of one species and 
distinguish them from others (the biological species 
concept) In many groups large numbers of species are easily 
recognizable, and, if investigated sufficiently, may satisfy all 
or several of these criteria. But in other groups and in other 
species, variation patterns may be obscure or insufficient 
information may be available: in some it may be difficult to 
find a workable species concept, in others a minority of species 
are in complexes where the boundaries are uncertain. It is, after 
all an amazing achievement even to attempt to categorize 
into comparable units organisms as different as elephants 
and bacteria. Despite the universal and successful usage of the 
species, its precise definition is, and probably always will 
be, the subject of vigorous debate within the taxonomic 
discipline. There is no scientifically precise, universally 
applicable species definition. In practice there is no choice 
but to pursue a pluralist approach, using where appropriate 
one or other of the three main concepts given above. 
A theoretical view is that each element in the 
classification is a hypothesis. This illustrates nicely the 
relation between the three main species concepts. The 
description of a species on the basis of the morphological 
concept is interpreted as hypotheses that (1) its unifying 
characteristics were inherited from common ancestors (the 
phylogenetic concept) and (2) there is in place some 
biological mechanism that maintains its distinctness from 
adjacent species (the biological concept). These hypotheses 
can then be tested. 
The time when the species was considered the smallest 
unit of variation observed is long past. Detailed observation 
and knowledge of genetics mean that today biologists are 
extremely conscious of the range of variation that occurs 
within each species (see Chapter 2.2), and of the 
possibilities for classifying subunits within the species - 
subspecies, varieties and informal races in the wild; or 
cultivar groups, cultivars and breeds under domestication 
(see Table 2.1-1). However, the morphological and 
phylogenetic species concepts do still depend on being the 
smallest unit that is clearly distinct, or clearly diagnosable 
2J.4.1 The morphological species concept 
The most widely used method of recognizing species is 
referred to as the morphological species concept, defined in Box 
2.1-4. The term morphological is, however, a misnomer as 
[he concept is applied to any sort of comparative 
information on heritable characteristics (Davis and 
Heywood 1963) such as data on behaviour, phylochemislry and 
microanatomy. In the ideal case there is continuity of 
variation within and a distinct discontinuity between 
species. In practice it is the presence of clear discontinuities 
such as a correlated discontinuity in two or more characters that 
circumscribes the species (Hedberg 1958; Davis and Heywood 
1963). Ideally all members will possess the diagnostic 
41 
characters of the species. In reality some species are 
polythctic, that is, defined by a combination of characters, 
any one of which might be absent in one member of the 
species, a property analogous to fuzzy sets in mathematics. 
A variant of this concept is the monatypic species, widely 
used in the great Russian schools of taxonomy Here 
emphasis has been on the smallest indivisible unit, that is. 
on uniform homogeneity within the units rather than clear 
discontinuity between them (Komarov 1944; Juzepczuk 
1958). Such a system was considered by some authors to he 
advantageous in floristic work and in inventorying natural 
or genetic resources: every recognizably distinct form is 
named and catalogued separately. 
A special case is used in the recognition of bacterial 
species where there are few morphological features. The 
DNA/DNA hybridization technique is used to assess the 
DNA resemblances of different bacterial strains. Strains 
with DNA resemblances above 70% are treated as 
members of the same species. 
2.1.4.2 The biological species concept 
In the ninteenlh and early twentieth centuries attention 
turned to species as biological units, giving rise to what we 
now call the biological species concept (defined in Box 
2.1-5). The concept emhasizes interconnected populations 
of interbreeding organisms. The key criterion for delimiting 
species boundaries is reproductive isolation (Vavilov 1931; 
Mayr 1963, 1970; Zavadsky 1968). The classical literature 
also refers to the polytypic concept, referring to something 
broadly equivalent to the biological species (Vavilov 19.31; 
Box 2,1-4: Morphological species concept. 
Morphological species concept (Du Rietz 1930; Cain 
1954; Mayr 1963; Shaw 1964) 
The smallest natural populations permanently 
separated from each other by a distinct discontinuity 
in the series of biotxpes. 
Comment: The concept most commonly used by 
practising systematise. Many schools of application 
suggest a minimum of two correlated characters to 
characterize a sufficient discontinuity. 
Criticism: Morphological or comparative criteria may 
not reflect actual links thai hold organisms together into 
a natural unit In sexually outbreeding organisms, some 
morphologically distinctive forms can freely interbreed 
to produce healthy, fertile offspring while other similar 
forms do not interbreed Well known cases include 
cryptic species, polytypic species and ecophenotypes 
(Mayr 1963, 1982). 
42 Characterization of Biodiversity 
Box 2.1-5: Biological species concepts. 
Biological species concept I (Dobzhansky 1937; Mayr 1940. 1969) 
A species is a group of interbreeding natural populations that are unable to successfully male or reproduce with 
other such groups. 
Comment: One of the most popular species concepts because it conforms to the popular view of how evolution 
occurs. An important point of this definition is that .species are not distinguished by degree of difference, but by failure 
to reproduce with other species. Two species may appear extremely similar, but if they do not interbreed then they are 
two distinct species. 
Criticisms: 
(a) It is irrelevant to asexual or parthenogenetic organisms where reproduction occurs without interbreeding even 
though their role in the ecosystem is the same as sexual species. 
(b) Relaiedness and ability to reproduce are not always tightly linked (Rosen 1979; Baum 1992), 
(c) The amount of interbreeding between groups varies and it is not clear how much is necessary to identify two groups 
as belonging to the same species or how little indicates that the two are separate species. This question has been 
particularly troublesome in botany where phenomena such as natural hybridization, polyploidy, apomixis and 
interspecific introgression (see Chapter 2.2) complicate the delimitation of species (Levin 1979; Grant 1981). 
(d) Although the biological species concept may be accepted by biologists as an accurate description of what species 
are, it may not be used in practice by systematists because it can rarely be applied to real groups of organisms. Often 
reproductive isolation is inferred (not observed) from the absence of individuals with intermediate characteristics 
between two groups or by making assumptions about specific evolutionary processes (Mishler and Brandon 1987). 
Interbreeding is very difficult to observe in nature especially if groups are geographically or tempotally separated. The 
systematist is effectively left having to guess whether groups would interbreed if they were living in the same time and 
place. Simply bringing the groups together in captivity or cultivation and seeing if they will cross is not sufficient as it 
is well known that under such artificial conditions many organisms will fail to breed even if they are members of the 
same species in the wild. Furthermore, separate species may breed in artificial conditions, even if they would not do so 
in the wild. 
Biological species concept II (Mayr 1982) 
A species is a group of interbreeding natural populations unable to successfully mate or reproduce with other such 
groups, and which occupies a specific niche in nature. 
Comment: The introduction of 'niche' broadens the original biological species concept to include asexual and 
parthenogenetic species. 
Criticisms: Criticisms b, c, and d of the biological species definition 1 (above) also apply to this concept. 
Furthermore, problems with defining 'niche' make this concept hard to apply in natural settings (Hcngeveld 1988). 
Recognition species concept (Paterson 1978. 1982, 1985; Vrba 1984) 
A species is a group of organisms that recognize each other for the purpose of mating and fertilization. 
Comment: This concept shifts attention from isolating mechanisms as barriers to breeding, to features that facilitate 
breeding among members of a species It is supposed that the systematist is able to deterrhine what features are 
important to the organisms in mate recognition. If this is possible, one could distinguish natural species in the same 
manner that the organisms do. 
Criticism: Determining whether a feature is used to recognize potential mates is difficult or impossible to do in 
many wild populations. Furthermore, species that occasionally form hybrids would he considered the same species by 
this concept (Butlin 1987). 
Characterization of Biodiversity 43 
Cohesion species concept (Templelon 1989) 
The smallest group of cohesive individuals that share intrinsic cohesion mechanisms. 
Comment: Like the biological species concept and the recognition species concept, the cohesion concept accepts 
interbreeding ability as a mechanism that binds organisms into a group In addition, it recognizes other mechanisms, 
such as niche requirement, as causing cohesion too 
Criticism: Cohesion is operationally difficult to recognize and applying this concept to problems of recognizing 
species in nature is almost impossible. Furthermore, it is not clear how to interpret varying degrees of cohesion 
between groups (Rndler 1989) 
Ecological species concept (Van Valen 1976) 
A lineage which occupies an adaptive zone different in some way from that of any other lineage in its range and 
which evolves separately from all lineages outside its range 
Comment: The ecological species concept supposes that niches are discrete adaptive zones with gaps between If an 
organism whose attributes adapt it for life in one of the gaps between niches will be maladapted: it will be fit to exploit 
resources that do not exist, or to avoid non-existent parasites or predators. 
Criticism: Adaptive zones may be difficult to define in the real world, making this a difficult concept to apply 
practically. Furthermore, it is based on the often false premise that two species cannot occupy the same niche even for 
a short period of time (Wiley 1978). 
Zavadsky 1968; Takhtajan 1984; Agaev 1987). In some 
cases a complex pattern of various forms is bounded by 
a discontinuity and the taxonomist infers, but 
without experimental work, that this is one polymorphic 
biological species. 
The biological species concept has functioned well when 
applied to the major well-known groups of sexually 
outbreeding organisms. Indeed the link with population 
genetics and ecology had proved so robust that to many 
experimental and field biologists this has become the true 
species that exists as a biological unit, and whose 
membership can be determined by biological testing (see 
Chapters 2,2 and 2.3). What are often forgotten, however, 
are the real limitations on the applicability and functioning 
of the biological species concept (see Box 2,1-5). By its 
very definition it can only be applied to organisms with 
sexual breeding, and a large number of organisms do not 
fall in this category. Reproductive isolation also proves to 
be incomplete in some groups: it is particularly in plants 
'hat natural hybridization, introgression, the formation of 
polyploids from hybrids, and hybridization between 
polyploids (see also Chapter 2.2) all create circumstances 
where there is no clear demarcation (Stebbms 1950; Gram 
'"81). Manipulation of these mechanisms is of intense 
interest to plant breeders (sec Chapter 2.2) and has lead to 
development of the gene-pool concept (Harlan and de Wet 
ly?l), where Gene pool I, (Figure 2,1-6), Gene pool 2, and 
Gene pool 3 represent various outer levels of hybridization 
ar>d ocasional gene flow. But even this eminently practical 
scheme can be challenged on the basis that in nature there 
are many examples of populations separated by only a few 
kilometres that rarely if ever exchange genes (Ehrlich and 
Raven 1969; Levin 1979). 
2.1.4.3 The phylogenetic species concept 
A second set of species concepts views species as the 
terminal twigs on the evolutionary tree. Speciation is the 
process by which new lineages originate. Similar 
figure 2.1-6: The gene-pool concept proposed by Harlam and de 
Wei (1971). Satisfactory only after ail the tax a concerned have 
been intensively studied and satisfactorily classified 
44 Characterization of Biodiversity 
Box 2.1-6:  Evolutionary species concepts. 
Evolutionary species concept (Simpson 1951, 1961; Wiley 1978} 
A species is a single lineage of ancestor-descendant populations which is distinct from other such lineages and 
which has its own evolutionary tendencies and historical fate. 
Comment: This broad definition is intended to define species in terms of the evolutionary process and would thus 
include living, extinct, sexual and asexual organisms. 
Criticism: The concept is difficult to use when trying to identify species in nature because the criteria - evolutionary 
tendency and historical fate - are vague and difficult to observe (Hecht and Hoffman 1986). 
Phylogenetic species concept (Rosen 1979; Eldredge and Cracraft 1980; Nelson and Platnick 1980; Cracraft 1983; 
Nixon and Wheeler 1990, 1992) 
A species is the smallest group of organisms that is diagnosablv distinct from other such clusters and within which 
there is a parental pattern of ancestry and descent. 
Comment: This concept focuses on the phylogenetic history of organisms and considers a species to be the last 
diagnolsable or undivided twig on a phylogenetic tree. 
Criticism: As pointed out by Wheeler (1990), application of the phylogenetic species concept would almost certainly 
give far greater estimates of the total number of species than the more traditional biological species concept. As tax a 
are examined in more detail (especially with molecular genetic techniques), the chances of finding slight differences 
between small subgroups increases, and those would be named as separate species under this definition. 
organisms, regardless of mode of breeding, owe elements 
of their resemblances to inheritance from a common 
ancestor. We thus have the evolutionary species concept 
(Simpson 1951) and the phylogenetic species concept 
(Cracraft 1983) (see Box 2.1-6). A difficulty, at least in 
long time-spans, is that an evolving species may eventually 
become so different that it can be considered a different species. 
At what point in time is the separation made (Lovtrup 
1979)? In practice these concepts again recognise species 
on the basis of distinguishing characteristics: the results may 
not be much different from applying the morphological concept, 
in some cases, the emphasis is placed on the smallest 
phylogenetic element, so that, as with the monotypic 
concept, each recognizable unit may become a species. 
A special form of the phylogenetic species concept has 
been adapted (ICTV 1991) for the definition of virus 
species. A virus species is a polythetic class of virus that 
constitutes a replicating lineage and occupies a particular 
ecological niche (Van Regenmortel 1990). The niche of a 
virus can often he quite clearly demarcated by 
environmental determinants such as host, tissue and vector 
tropisms (Franki el at. 1991). 
2,1.4.4 The pluralistic approach 
One can argue that for the whole of species diversity to be 
built on such an uncertain unit as the species is very 
unsatisfactory. It is, however, the best: the only unit that we 
have' Because many patterns of variation are found in 
nature, a pluralistic approach to species demarcation is 
necessary to answer to the needs of taxonomists and other 
scientists working with different groups of organisms 
(Mishler and Donaghue 1982). 
The vast majority of species are still recognized by 
taxonomists on the basis of observed discontinuity (the 
morphological species concept). Experimental investigation 
of breeding patterns and careful phylogenetic analysis 
enrich our knowledge and in many cases clarify species 
circumscriptions, but they are too expensive to apply to all 
species. In practice the classical process is cheap, effective 
and answers most needs. 
One practical effect of the debate on species definitions 
is that the species concepts actually applied may be broader 
or narrower at different times or between taxonomists in 
different places. What are described and given the rank of 
separate species in one treatment may sometimes be 
aggregated into a single more inclusive species in another. 
Units given originally as separate species may then be 
described and named by another author as subspecies or 
varieties within one broader species for example, several 
species of peas (wild species Pisum elatius and Pisum 
humile, and cultivated species Pisum arvense and Pisum 
sativum) were subsequently found to be interfertile and 
thus thought of as members of just one species (now Pisum 
sativum) using the biological species concept (Makasheva 
1979). However, the originally discernable units are now 
referred to as botanical varieties within the one species (eg- 
Characterization of Biodiversity ?75 
Box 2-1-7: Different layouts for printed classifications, (a) is part of a Checklist giving a linear listing of taxa 
fforbet & Hill 1991). (6) is part of a Flora showing the taxa again in linear sequence but now with descriptions and 
keys included in the sequence (Tutin et a! 1964-80). 
(a) Checklist layout. SUBORDER MICROCHIROPTERA 
Family Rhinopoma tidae 
Mouse-tailed bats (rat-tailed bats, long-tailed bats); 1 species; Morocco, Senegal 
Thailand, Sumatra, mainly desert and steppe; insectivorous. 
Greater mouse-tailed bat 
(Rhinopoma microphyllum) 
Rhinopoma 
R. hard wick ii 
R. microphyllum 
R. muscatellum 
Lesser mouse-tailed bat 
Greater mouse-tailed bat 
Morocco, Maurctania, 
Nigeria - Kenya - 
Thailand 
Senegal  - India; Sumatra 
S Arabia - W Pakistan 
Family Emballonuridae 
Sheath-tailed bats (sac-winged bats, pouched bats, ghost bats); c. 49 species; 
tropics and subtropics of world; insectivorous 
Subfamily Emballonurinae 
Sac-winged bat 
(Saccoptcryx biiincata) 
(b) Flora or Fauna layout 
Emballonura; 
Islands. 
E. alecio 
(rivalis) 
E. atrata 
E. beccarii 
E. dianae 
Old-world  sheath-tailed  bats;  Madagascar,  S  Burma   -  Pacific 
Philippine sheath-tailed 
bat 
Peters' sheath-tailed bat 
Beccari's sheath-tailed bat 
Rennell Island sheath- 
tailed bat 
Philippines, Borneo - 
S Moluccas, Tanimbar 
Is; ref 4.143 
Madagascar 
New Guinea, etc. 
New Guinea, New Ireland, 
Malaita, Rennell Is, 
Solomons; ref. 4.26 
CLXVJI. DIPSACACEAE1 
Annual to perennial herbs, rarely shrubs. Leaves opposite or 
verticil [ate, exstipulate. Florets in a dense, cymose capimlum 
subtended by involucral bracts, often with marginal flowers 
radiate, rarely in a spike of verticiWasters. Florets hermaphrodite 
or female, usually zygomorphic, each with a basal epicalyx 
(involute!) of connate bracteoles which may be expanded dis- 
tally into a carona, often subtended by a receptacular scale. 
Calyx small, cupuliform or divided into 4-5 teeth or of numerous 
teeth or setae. Corolla-lobes 4-5, subequal, or corolla 2 lipped. 
Stamens 2 or 4, epipelalous, altemaiing with corolla-lobes. 
Ovary inferior, l-locular; ovule I, pendent; stigma simple or 
2-lobed. Fruit dry, indchiscent, enclosed in epicalyx and often 
surmounted by persistent calyx; seed 1, endospermic. with 
straight embryo. 
!    Inflorescence a spike of verticil lasters I. Morina 
i    Inflorescence of 1 or more capilula 
2   Stems with prickles 3. Dipsscus 
Z   Stems without prickles 
1
    Involucral bracts connate in basal half; calyx-setae presort 
only in central florets of capitulnm 10. Pycnocomoti 
3    Involucral bracts free; calyx-setae present or absent in all 
florets 
4   Calyx-selac plumose 
5    Fruiting involucel with longitudinal furrows runnmg the 
whole length 7. Ptfroceptalus 
1
 Edit   D. M   Moore 1
 By J, F- M- Cannon 
5 Fruiting involucel with R pits in distal half, furrowed below 
9. Tremastelma 
4   Calyx-setae absent or, if present, not plumose 
6 Calyx-setae or -teeth (6-)8-16(-24);  receptacle hairy, 
without scales 6. Knatitia 
6   Calyx setae or -teeth 4-5 or absent; receptacle not hairy, 
with scales 
7    Marginal florets radiate; corolla 5-lobed 8. Scabiosa 
7    Marginal and central florets subequal; corolla 4-lobed 
8    Involucral bracts in more than 3 rows 2. Cephalaria 
8    Involucral bracts in 1-3 rows 
9    Calyx-setae 4-5; involucel angled 4. .SuccLsa 
9    Calyx-setae absent; involucel ? terete 5. Suecisetia 
1. Morina L ! 
Perennial herbs. leaves verticiltale, spinose Inflorescence a 
spike of many-flowered, braclcalc vertici [lasters. Involucre long, 
infundibuliform, spiny. Calyx deeply 2-lobcd. Corolla with 
curved tube, distinctly 2-lipped. Fertile stamens 2, Fruit with an 
oblique apex, rugose. 
I. ML persica !_., Sp. Pi. 28 (1753). Robust plant 30-90cm. 
Leaves 15-20 x 1-2 cm, linear to elliptical, dentate to pinnatifid, 
glabrous. Vcrlidllaslcrs rather distant; bracts 2-4-5 x e, I cm, 
ovate-triangular, sometimes pinnatifid near base, with marginal 
spines up to c. 1 cm.  Calyx-lobes subequal, entire oremarginale 
'46 Characterization of Biodiversity 
P. salivum var elatii/s, etc.; Davis 1970). The reverse 
process can be seen with the application of phylogenetic 
species concepts to birds, where recognizably distinct 
subspecies under the biological species concept, usually 
geographical races, could be segregated into separate 
species using the phylogenetic concept. Regional 
inconsistency in assignment of the species rank by 
taxonomists can be seen in Flora Europaea (Tutin et at. 
1964-80), where species described by Russian botanists 
using a monoiypic concept have in a few instances been 
listed alongside wider species described by Western 
Europeans using the biological species concept. The broom 
genus Chamaecytisus is, for example, given as having a 
large number of narrow-concept species whose distribution 
stops abruptly at the boundary of the former Soviet bloc 
countries, and fewer broad-concept species west of this 
boundary. 
For the vast majority of species the exact definition used 
makes little difference to the unit circumscribed. Only for 
the minority, usually where there are clusters of similar 
forms, can the concept used have the effects described. But 
users of the taxonomy should be aware that total species 
numbers may vary from one treatment to another, and in 
some groups the question of rarity and endemism may 
interrelate with varying views of what constitutes species. 
This brings to an end our introduction to taxonomic and 
evolutionary characterization (2,1.0-2.1.4). What follows 
in Section 2.1,5 illustrates the wide and fundamental way 
in which the taxonomy underpins all knowledge of 
biodiversity: it provides a rich information structure and a 
picture of the natural map of diversity. Lastly, Section 2.1.6 
highlights the view of many taxonomists and evolutionary 
biologists that the mere counting of species is a rather 
uninformative and unrepresentative way of measuring 
species diversity. The taxonomy provides a map, and 
species diversity should be characterized as dispersion on 
this map, with particular value given to distant islands and 
wide-ranging spans. 
2.1.5 The power of (axonomy and taxonomic products 
2.1.5.1  Taxonomic products: an essential technological 
infrastructure for biotechnology, natural 
resources management, and regulation 
The single most important use of taxonomy is to provide 
the core reference system for organisms used throughout 
biology and its associated sciences and industries. The 
taxonomic classification is similarly the core reference 
system for biodiversity (Janzen 1993). This reference 
system is made available through the range of taxonomic 
products such as the Floras, handbooks and keys already 
discussed. The dissemination of certain basic information 
about the organisms is also traditionally incorporated with 
some of these, such as morphological descriptions and 
images of flowers and leaves for plants, maps plus 
behavioural and song descriptions for birds, etc. 
How are these products actually used to disseminate the 
reference system? Whilst there are many variations in 
detail, they are composed of just four principal features, 
each with its own function: 
(1) The classification. The classification is given either 
as a concise checklist or by the structure provided by the 
sequence of organism entries in the book, (see Boxes 2.1-7 
and 2.1-8). The classification provides reference 
information on the existence and taxonomic position of 
each organism. 
Much the commonest starting point is the name of an 
organism. From the name one can learn what the organism 
looks like, where it occurs, what other organisms have 
similar characteristics or are genetically related to it, and 
much else about its biology and role in the environment: 
the name and the place in the classification provide a 
vehicle through which this information is obtained. 
What if the enquirer does not know the name? In this 
case the enquirer must first go to the identification routine: 
find out the name of the organism under scrutiny The 
quest for further information can then be the standard one 
starting from the name. 
(2) The nomenclature. The nomenclature provides the 
scientific names used to label and retrieve organisms and 
groups of organisms. Users also need to be alerted to cases 
where an organism or group of organisms has previously 
been known by other names which can be treated as 
synonyms for the same. Because the names are needed to 
label the entries they are presented as part of the 
classification in products such as handbooks and Floras. 
Checking what the names are, and checking the spellings 
and authors are important infrastructure services for those 
dealing with organisms in many biological professions. 
Examples are given in Box 2.1-9. 
(3) Descriptions/circumscriptions. To be logically 
complete, a taxonomy needs to provide not only a 
statement about what are the taxa, but also to circumscribe 
the range of variation among organisms found in each 
taxon. In practice, detailed circumscriptions are often kept 
for the technical taxonomic literature, but descriptions 
giving a word picture of the organism, or images of various 
sorts are often included as shown in Box 2.1-10. This 
important feature means that using many taxonomic 
products a user can find out what the organism listed looks 
like. So the enquiries illustrated in the boxes above (to find 
species related to Vicia serratifolia. or to check the name of 
Broom) can lead to a description, illustration and 
geographical distribution information for the species in 
question, as illustrated in Box 2.1-10 
(4) Identification aids. A variety of devices can be 
provided so that the user can examine an unknown 
specimen  and  determine   where   it   belongs   in  the 
R6 
Characterization of Biodiversity 47 
Box 2.1-8: Examples of factual responses (hat can be 
obtained from the classification. 
(1) position 
Where does taxon X fit in the classification? In 
which order, class or phylum is it to be found? 
Response, if   X = Genus Apis (hive bees) - 
in the order Hymenoptera (bees, ants and 
wasps) 
in the class Ensecta (insects) 
in the phylum Arthropoda 
(2) Members of a set 
What other laxa resemble taxon Y? or What is the 
complete list of members of the taxon containing 
Y? Response, if Y = Vicia serratifolia 
- one of 7 species in Section Faba of genus Vicia 
-the 7 species are: 
Vicia narbonensis 
Vicia serratifolia 
Vicia johartnis 
Vicia gatitaea 
Vicia kalakhensts 
Vicia hyaeniscyamus 
Vicia faba 
(3) Subordinate taxa 
What are the members of taxon Z? or Provide a 
systematic catalogue of all members of taxon 2? 
Response, if Z = Genus Acetobacter 
Acetobacter aceti subsp, aceti 
Acetobacter aceti subsp. orleanensis 
Acetobacter diazoirophicus 
Acetobacter hansen.ii 
Acetobacter Uquefaciens 
Acetobacter pasteurianus subsp. ascendens 
Acetobacter pasteurianus subsp. estunensis 
Acetobacter pasteurianus subsp. lovaniensis 
Acetobacter pasteurianus subsp. paradoxus 
Acetobacter pasteurianus subsp. pasteurianus 
Acetobacter peroxydans 
Acetobacter xyiinum 
classification. The commonest device is the key (see Box 
2.1-11) in which the user answers a series of questions 
about contrasted descriptive features, and by elimination 
arrives at the identification of what the organism is. 
Z i.S. 2 As a summary of biodiversity and evolutionary 
patterns 
The taxonomy provides considerably more than the bare 
bones factual information system described above (the 
reference system): it also provides a summary of the pattern 
Box 2.1-9: Examples. 
What is the correct (accepted) name for organisms 
labelled X? 
e.g. it X = Sarothamnus scoparius (Broom) 
response: Cytisus scoparius 
(all species formerly known as Sarothamnus now 
usually included in Cytisus) 
e.g. if X = Vicia narbonensis var. serratifolia 
response: Vicia serratifolia 
(now accepted as a separate species) 
e.g. if X = Cytisus scoparius 
response: Cytisus scoparius 
(correct as given) 
Under what names has taxon Y been known in 
the past? 
e.g. if Y = Rattus exutans (Polynesian rat) 
response: Rattus exulans (accepted name) 
Rattus bocourti (synonym) 
Rattus ephippium (synonym) 
of diversity and of the pattern of evolution in a group of 
organisms. The patterns are to be seen in the tree structure 
of the taxonomic hierarchy. Consider for instance the 
partial taxonomic hierarchy of gymnosperms shown in 
Figure 2.1-7. 
The hierarchy depicted shows the reader that Ginkgo 
biloba (the maidenhair tree) is the only living 
representative of the order Ginkgoales, and that it is thus 
very isolated and distinct in terms of diversity from the 
nearest other group, the Coniferales (Conifers). Conversely, 
the Conifer ales is made up of seven families, each of which 
contains several genera and many species, amounting to a 
total of 610 species (Mabberley 1987). For instance, the 
Pinaeeac (Pine family) contains 10 genera, of which Pinus 
contains about 120 species world-wide and Abies 55 
(Rushforth 1987). Pinus and Abies species are thus 
nowhere near being so isolated as Ginkgo biloba: each 
species has a number ol other species so close or similar as 
to be in the same genus, and a number ol close or similar 
genera exist within the same family and in six related 
families. This then is the description of a pattern of species 
diversity. This diversity pattern allows us to quantify the 
diversity of, say. forests composed of just two species of 
gymnosperm: the forest whose two species are both pines 
(Pinus spp.) has low diversity (they are both in the same 
genus), the forest with one Pinus and one Abies comes next 
(its species are in related genera of the same family), whilst 
48 Ch a rac teriz a t ion of B i odi versky 
Box 2.1-10: Examples of descriptions, illustrations and maps from Greenwood 1987 (a), and Valdes et al. 1987 (b) 
The description in a) is part of a 'diagnosis" or "circumscription", an exact complete technical description of the 
animal. The description in b) is a brief synoptic description that could be used by botanists in general 
(a) Part of a diagnosis1 and illustrations from Greenwood 1987. 
Fig. 21    Parananoehromi$ hngirostris; hololypc. From the original drawing by J. Green. 
Scale bar in mms 
Hi S     Ki^hl jnfnorbiliHranriDr A  fttmajafhimny imeuA?fer\{\U:hfyital ftnly], B. Ch'amuiwdtpia 
PfJufOfAfOmr..! puittir* 1 ll?h'yirti I 4 I aiheraj, ?. Thri 10 an iiwjir {L*f hr)iPJ I 4 * OIFKP^I  Scab tut 
(6) A description, map and illustration from Valdes et al. 1987. 
3. Polypodium iuterjectum Shivas, Journ. 
Linn. Soc. London (Boi.) 58: 29 (1961) 
P. uulgare subsp. prionodes (A sc he rs o n) 
Rothm., Mitt. Thuring. Bot. Vereins 
38: 106(1929) 
P vulgare aucc, non L., Sp. PI. 1085 
(1753) 
Rizoma mas o menos largo con escamas 
cicnsa5. Hscamas de(2) 3-6 (-8) mm, linear- 
ianccoladas Hojas de (1 4-) 1 7-22 (-30) cm, 
limbo generalmente mas largo que el pecio- 
lo. con la anchura maxima hacia la mkad, 
de ovado a ovado-lanceolado, gradualmen 
(c acuminado. Pinnas agudas Soros elip- 
[icos, sin pa ran sos, a veces con pclos 
glandulares. Anillo del esporangio con (4-) 
7(13) celulas engrosadas y 2-3 celulas en 
la base. 2n = 222. Esporula de Julio a Sep 
tiembre. 
Muy fify Kupk\rfa Algeciru 
Distribution general R^ginrics 
Eurosibcraru i- Mfdirarincj 
Characterization of Biodiversity 49 
?     2*1-11: Two examples of printed indentirication keys, (a) 'indented' type - the first two contrasting Jeads 
re labelled *T; if the lower of these is selected, the next pair labelled 42' are indented, and so on. (b) I he 
?bracketed' type, where the contrasting leads are printed (or sometimes bracketed) one below the other, J2 and 
its partner, J3 and its partner, etc. 
Indented key to genera Turkish Gymnospcrmac (Davis 1970). (h)    Bracketed key to hcellc families of Britain (Unwin 1984). (fl) 
SPERMATOPHYTA 
GYMNOSPERMAE 
Kratisc. K. 1936 "ntrkiyatin Gytttnospermteri. Ankara. Kayacik.H. \959, Or man 
pork AiQfi&inin Oitl SisfernQtigi. I. Cilt: Gymnospermae (Acik Tohumtar). 
Istanbul 
Key to Genera 
1   Leaves reduced to scales at the nodes; equisetoid shrubs {Ephedraceae) 
Kpfirtlra 
1, Leaves not reduced to scales al (he nodes; trees or shrubs, not equisetoid 
2   Mature leaves scale-like, imbricate and ad pressed, or linear- Lanceolate and 
articulate at the base {Cupressaeeae) 
Z- AH leaves scaJe-like and imbricate; fruit a woody cone; seeds winged 
Cuprcssus 
3   At least the juvenile leaves linear-lanceolate, not scale-like and imbricate; 
Fruit fleshy, berry-like; seeds unwinged Juiperus 
2. Mature teaves oblong-linear, not articulate at the base 
4, Leaves without resin canals; fruit surrounded by a fleshy aril (Taxaceae) 
A. Leaves with resin canals; fruit a woody cone, cxarilUte (Pmaceae) 
5. Mature leaves borne on short shoots, in whorls or fascicles of two 
6. Leaves in fascicles of two, each fascicle surrounded by a sheath at the 
base Pinus 
6. Leaves in whorls, without sheaths at ihc base Cedms 
5. Mature leaves borne spirally on long shoots; short shoots absent 
7. Branch lets with numerous peg-like projections persisting after leaf fall; 
cones pendulous, falling as a whole Pices 
7. Branch lets without such projections; cones erect, the scales falling from 
the persistent axis Abies 
Bt<ll<? with cly|fa covering most of the abdomen. Antenna? clubbed, and i?rii 
wich tame segment; lobed beneath. 
Number of drill JcgimcntS- 
Nott: in Ehii kty, inulL tyNndiisiil lutil I 
igiWftJ   r.Ji*T (VnOt CCuKll II ttgineME 
Tirut chjirxlrn nufbc ciaicr w ict if a J 
Tarn wJ[K 5 segments . 
Tarsi with 4 segment! . 
Tarsi with J segments . 
J2 
15 
[19 
Thorax constricted basalty, beetles with i 
very obvious "waist" Tborai ^ilh out- 
standing long hair! . CLERJPAE 
Beetles without a distinct ' 
[':?-:J* and elytra 
be I ^een 
n 
Eyes  oval,  over  twice  as   high as  wide, 
occupying mosi of ihc hcighl of the head 
 BUPRESTIDAE 
Eyes approximately circular M 
Oval beetles WHO a wide turned-out rim to 
the elytra and the thorax giving a terrapin- 
like appearance T.btae not flattened and 
expanded PfcLTIDAE 
Beetles with at most a narrow "beading" 
on thorax and elytra. Tibiae flattened and 
expanded EROTVL1DAE 
the forest (if such were to exist) with one Pinus and Ginkgo 
biioba has a relatively enormous diversity, because its two 
species are in separate orders. This patterned or qualitative 
view of diversity provides the basis for taxonomic or taxic 
measures of diversity discussed in the next section. 
The same classification hierarchy can be taken to imply 
the shape of the evolutionary tree or phylogeny. For 
instance, two elements of the evolutionary pattern might be; 
1. that Ginkgo separated from the evolutionary line of 
conifers at an early date, and 
2. that members of the Coniferales are thought to be 
monophyletic, that is with a common ancestor more 
recent than the one they share with Ginkgo and with all 
the descendants of thai common ancestor included in the 
Coniferales group. 
However, as noted earlier, the taxonomic hierarchy can 
at best only loosely mirror the branching pattern of the 
cladistic tree. A more precise view of the hypothesized 
route of evolution will be obtained by examining in 
addition any published phylogenies for the group 
2.1.5.3 As u basis for prediction 
The natural pattern reflected in the taxonomy enables 
scientists to make predictions about as yet unobserved 
features of organisms These predictions are only 
probabilistic, but they can provide a powerful and 
economically important basis for directing future biological 
research. One example is the successful search for 
casianospermine-like substances of possible significance in 
HIV research in South American legume plants of the genus 
Aiexa. The substances were first discovered in an Australian 
plant cultivated in South Africa. This was Castanospennum 
austrate (Moreton Bay chestnut), the only species at that 
time in the genus. When phy toe he mists wanted to look for 
the substances in other plants, taxonomists predicted that the 
highest chance of finding similar properties would be in 
geographically distant Aiexa. a South American group but, 
taxonomically. the closest genus to Castanospenmwi. The 
prediction was correct and substances related to 
castanospermine were successfully isolated from the South 
American plants. In contrast, the chances of locating the 
substances rapidly by a random (and consequently 
expensive) search amongst the 280 000 or so Flowering 
Plants, or indeed amongst the   1.75  million  known 
50 Characterization of Biodiversity 
GYMNOSPERMAE (Subclass) 
Conifetales 
(610 species) 
Cupressaceae        Pinaceae 
Ginkgoales 
{1 species) 
Gtnkgoaceae 
?Uulc-M 
(Family) 
Abies Pinus Ginkgo (Genus) 
il I 
55 Abies spp. 120 Pinus spp Ginkgo biloba 
1 species 
(Species) 
Figure 2.1-7: Partial taxononuc hierarchy of [he Gymnosperms. 
organisms, would clearly be very small. A similar example 
is taxol, a drug used to treat ovarian and breast cancer, first 
discovered in bark extracts of the Pacific yew tree, Taxus 
brevifolia. Unfortunately the yield from one tree is small, so 
that harvesting sufficient quantities from trees in the wild 
was likely to endanger the species. But, using the taxonomy 
to predict which other trees might contain taxol, scientists 
quickly discovered that the European yew tree, Taxus 
baccata, gave a much higher yield and is easily cultivated in 
quantity. Harvesting from this species causes no damage. 
Another predictive feature relates to the ability to 
hybridize species or use other means to transfer 
economically important genes. The taxonomy can predict, 
again probabilistically, in which organisms wc may 
successfully find genes that can be transferred to a target 
species, such as a crop, and be found to function 
successfully within that target species. Thus, in seeking to 
reduce virus susceptibility of cultivated corn {Zea mays), 
plant breeders turned to the recently discovered related 
wild species Zea diploperennis from Mexico as a source of 
resistance genes. Resistance to seven viruses was located 
and virus-resistant forms incorporating 2. diploperennis 
genes are now grown in South Africa (Raven et al. 1992). 
2.1.5.4 Other uses of taxonomic techniques 
The techniques developed for deducing phylogenetic trees 
have proved useful in a number of contexts outside the 
mainstream of biodiversity assessment. One of these is 
tracking sources of HIV. The HIV virus mutates so rapidly 
that a reconstructed phylogenetic tree can be used to track 
both human infections and the passing on of laboratory 
sources over very short time-scales. One classic case was to 
determine whether someone was infected from an HIV- 
positive dentist or from a different source, and another was 
to show that Robert Gallo's research discoveries in the 
USA were made on HIV sources from a competing 
laboratory in France (Wain-Hobson et al. 1990). 
Phylogenetic tree reconstructions of mitochondrial DNA 
sequences have also been used in the support of the Eve 
Hypothesis, that all humans originate from Africa (Vigilant 
and Stoneking 1991), Mitochondrial DNA is maternally 
inherited, so the tree tracks back through ancestral mothers 
Characterization of Biodiversity 
a postulated African female, ancestral to all modern 
mans. Another use is to reconstruct the evolution of 
omplex molecules where different variants of (he 
molecule are present in the same organism: a classic 
example is the evolution of globin and haemoglobin 
molecules (Jeffreys 1982) 
2 1.6 Taxonomic measures of species diversity 
A matter for substantial debate is the question of whether 
all species, or indeed all higher taxa (families, genera, etc.), 
are to be valued equally. As described in Chapter 2.3, the 
most widely used measure of within-area diversity is 
species richness, a simple count of the number of species 
present, or the diversity of an ecosystem. All species are 
thus counted as equal, In contrast, there is a view that 
individual species vary enormously in the contribution they 
make lo diversity because of their taxonomic position, and 
that as a consequence measures of ecosystem diversity 
should include a taxonomic measure of diversity amongst 
the species contained. Two particular arguments are the 
widely expressed view (IUCN 1980) that taxonomically 
isolated species or species of isolated genera are of high 
value (such as the ginkgo, Ginkgo biloha, the tuatara, 
Sphenodon, or the coelocanth, Latimeria chalumnae) and 
that when valuing sets of species, a wide taxonomic range 
of species encompasses more species diversity than an equal 
number of closely related species from the same genus. 
Faith (1992) introduced the concept of feature diversity and 
links this to the discussion on option value and conserving 
variation for future use (McNeely et al. 1990). 
Although most taxonomists and evolutionary biologists 
have clear concepts of taxonomic isolation and of 
taxonomic diversity, there were until recently no precise 
measures by which these concepts could be quantified. 
Initial suggestions by May (1990), Faith and Cawsey 
(1990) and Vane-Wright et al. (1991) led to proposals for a 
quantitative framework which is further developed, along 
with examples of application to conservation evaluation, in 
the symposium volume Systematics and Conservation 
Evaluation (Forey et al. 1994). 
2.1.6.1 Evaluating taxonomic isolation of individual 
species 
The traditional method of referring to isolated species has 
been to label a taxon in the classification as monotypic: a 
monotypic genus, monotypic tribe, monotypic family or 
monotypic order contains just one species. A quantitative 
scale, analogous to what is called node counting (Faith 1994) 
is implied in this measure. For instance, use of the phrase 
monotypic genus implies that the one species is isolated at 
one level of the taxonomy, but maybe not at the next level, 
where this and other genera may belong to the same tribe. 
Monotypic family (one species in a family) means that the 
tribe and genus levels must also be monotypic, so this family 
51 
is monotypic at all three levels. Examples include Ginkgo 
biloba, sole species in the Ginkgoaceae discussed above, the 
fem Loxoma cunninghamii (New Zealand), sole species, in the 
genus Loxoma, and many others. The node-counting analogy, 
however, is obscured by the fact that taxonomists do no! 
bother to name monotypic taxa at many ranks for a single 
species as it would serve no purpose, whereas in species-rich 
groups they use many intermediate ranks (subfamily, tribe, 
subtribe, subgenus, section, subsection). Whether or not a 
group is monotypic must be seen in relation to a time frame. 
The Ginkgoaceae, for instance, is monotypic today, but other 
now extinct species occurred earlier in the fossil record. 
The monotypic measure is a measure of isolation from 
the isolated species to the nearest other species in the 
classification, or if the tree is derived from a phylogeny, 
from the closest related species. Several authors (Faith and 
Cawsey 1990; Crozier 1992; Faith 1992; Weitzman 1992) 
have proposed quantitative measures of species 
distinctiveness. The method of Faith (1992) measures 
spanning subtree length (distance along branches of the 
phylogenetic tree) between an isolated species and its 
closest related species, ideally measured on a fully worked 
phylogeny. Where a phylogenetic tree is not available Faith 
suggests using the distances along branches of the 
classification tree, effectively node counting as with 
traditional monotypic statements. 
These measures may be used in conservation evaluation 
where a set of species is already protected (e.g. by law, 
within other reserves, in other countries), to evaluate which 
is the most isolated species whose additional protection 
would add most to the set already conserved. Faith (1992) 
Figure 2,1-8: A map of Australia showing botanic regions. 
Numbered regions are those making high contributions to 
phylogenetic diversity (from Faith 1994). 
52 Characterization ofBiodi 
antelope 
Higher- Lax on 
richness 
unrooted 
Spanning-subtree 
length 
rooted 
Spanning-subtree 
length 
Dispersion 
Figure 2.1-9: Classification of eight surviving species showing which biotas of just three species would score most highly when using 
each of the measures of taxonomic diversity. The selected species are shown by black spots, with any equally highly scoring 
alternatives for each choice shown bracketed by dotted lines The groups within the classification that are essential to represent high 
diversity value using each measure are shown in black, groups which remain alternative choices are shown stippled, and groups which 
are of low diversity value arc shown in white outlined in black (from Williams & Humphries 1994). 
describes using his measure to evaluate orchid floras in 
Australia. Thirty-two species and two endemic genera, 
Tnchoglottis and Aphyllorchis, occur in the Cape York 
region (Region 40 in Fig. 2.1-8). He applies his measure (to 
the albeit poorly known phytogeny of orchids) to evaluate 
which of the 71 regions contains other orchid species 
whose degree of taxonomic isolation would add most if 
added to the protected set. Region 63 (Central Coast, New 
South Wales) and Region 1 (SW Western Australia) add 
most, followed by Regions 53, 66, 67 and 71. The result is 
interesting both because of the evident complementarity 
implied (Regions 40, 63 and t are at diametrically opposite 
comers of Australia with widely different habitats), and 
because the ranking of evaluations was different from that 
obtained by valuing numbers of endemic species, the 
species traditionally thought of as valuable or at risk. 
Complementarity means that effective conservation of a 
valuable subset of taxa requires attention to conserving 
4^ 
Rhynchoceprialra Amohis&aenia 
30 sop 
Eusquamaia      Aclioislia 
5670 spp 1 sp 
Telrapods 
21.450 r.pp 
Figure 2.1-10: (a) Systematic position of Sphenodon (see Daugherty et at. 1990). Inset indicates geographical distribution of 
Sphenodon, restricted to the islands of New Zealand, (b) Systematic position of Latimeria (see Rosen et at. 1981). Inset indicates the 
geographical distribution of Latimeria, restricted to deep water habitats off the islands of Grande Comorc and Anjouan 
T** 
Characterization of Biodiversity 
xonomically different, complementary taxa often in 
d'fferent habitats, rather than focusing on single species 
hot-spots or areas of endemism. 
? 1 62 Measuring taxonomic diversity of biota or 
ecosystems 
Williams and Humphries (1994) review the methods 
proposed for measuring the taxonomic spread or diversity 
covered by a set of species, such as those in a single 
ecosystem or biota. They too assume that the methods will 
be most widely applied to the taxonomic hierarchy itself, 
although in some cases a phytogeny may be available. The 
differences between the measures are illustrated in Figure 
2.1-9, taken from their paper, which illustrates how 
different measures would lead to the selection of different 
species for conservation in an example set. 
It has been suggested that a key element in taxonomic 
diversity is the number of higher taxa present, or to focus 
on the basal taxa in a phylogeny or cladistic tree (Williams 
et al 1991; Stiassny 1992). Stiassny and de Pinna (1994) 
have reported an intriguing number of cases of high-level 
phylogenetic asymmetry where the basal taxa on a tree are 
both monotypic or bi-typic relict species, and endemic, and 
rare, such as Sphenodon and Latimeria illustrated in Figure 
2.1-10. Endemism and rarity are eco-geographic features, 
however, largely unrelated to taxonomic isolatedness. Two 
of the measures that take into account higher taxa, the root 
weighted method of evaluation (Vane-Wright er al. 1991) 
and the higher taxon richness method (Williams et al. 
1991), are illustrated in the comparisons in Figure 2,1-10. 
Versions of a direct measure of taxonomic spread have 
been proposed by Faith (1992), as the node-counting 
version of phylogenetic diversity, and by Williams et a!. 
(1993) as cladistic path length. Both can be referred to as 
spanning-subtree length measures. The number of nodes on 
the taxonomic tree needed to link the taxa is counted, each 
node being counted only once. 
Finally, Williams and Humphries (1994) have attempted 
to refine spanning sub-tree length with their cladistic 
dispersion measure which values an even representation, or 
evenly dispersed taxa where alternative biotas would 
otherwise tie on spanning sub-tree length The method is 
again visualized in Figure 2 1 -9. 
2-1.7 Conclusion 
1. Taxonomy provides the core reference system and 
knowledge base on which all discussion of biodiversity 
hinges, providing the framework within which 
biodiversity characterization occurs. Taxonomic 
characterization for all known organisms is a mammoth 
out essential infrastructure task with which only limited 
progress is being made: just 1.75 of the estimated 13 
million species have so far been described, and most of 
53 
these are still poorly known in biological terms. There is 
not even a comprehensive catalogue of these 1.75 
million known species. 
2. Systematic and evolutionary studies are now providing 
valuable knowledge about the phylogeny of life, the 
scientific map of diversity. This is the map on which 
conservation, prospecting, exploitation, regulation 
and sustainable use must be planned and, indeed, 
without which all might be lost. [( is important that 
assessments used in the evaluation of resources and 
conservation options make adequate use of taxonomic 
diversity measures that do take into account the 
positions and differing contributions made by different 
species. 
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2.2 Genetic diversity as a component of biodiversity 
2.2.0 Introduction 
In this Chapter we outline various aspects of biological 
diversity within the species. This diversity is variously 
termed subspecific (meaning below the species level), 
intraspecific or infraspecific (both meaning within the 
species, but the former term apparently more favoured by 
zoologists and the latter by botanists). A major aspect of 
(his is obviously what is termed genetic diversity (see 
below), but it should be borne in mind that within biology, 
genetics and systematic; are, or at least should be, 
intimately linked and that there are a considerable number 
of groupings below the species level which have taxonomic 
or systematic implications without necessarily being clearly 
defined in genetic terms. A number of the subspecific 
groupings more commonly referred to are outlined in Box 
2.2-1. Some of these (e.g. subspecies, varieties) are or have 
been used as straightforward subspecific taxa. Others (e.g. 
ecotypes, chemotypes) imply differences based upon other 
than conventional systematic characters or (e.g. cytoiypes, 
hybrids) have mainly genetic implications. The 
explanations suggested for these terms are not intended to 
be strict definitions and for many of them the intended 
meaning differs, often subtly, between authors and between 
fields of research and some, like the organisms they 
describe, have evolved with time and may no longer be 
used in precisely the same sense as they were by earlier 
workers. However, irrespective of meaning and usage, such 
intraspecific groupings generally can be assumed to imply 
some, albeit imprecise, level of genetic differentiation or 
genetic biodiversity. 
Genetic diversity is a critical component to issues of 
biodiversity. It is the genetic diversity within species that 
a lows a species the opportunity to evolve under changing 
environments and selection pressures. This section will 
overview the main fields of evolutionary genetics as 
aPpIicd to the assessment of biodiversity and introduce 
57 
briefl 
North w 'n&s 
Divergent wingj 
Ttimorous abdomen 
Benign nibdornirmt 
furriorj 
CrcrisY*inJ?a wins 
[SrCrmJ [ hJorrTul 
BUl? female 
Drcra^ft Ss FnfltfmJgfiSkr 
y various techniques available to assay genetic 
diversity within and bet ween species. 
Figure 2.2-1: Examples of some phenotypic variants found in 
natural Drosophila metanogaster populations: sketches of normal 
flies are presented for comparison. A relatively small proportion 
of such abnormal flies owe their abnormality to single mutant 
genes (from Hard and Clark 1989). 
The variability that we observe among individuals 
(phenotype) results partly from the interaction of genetic 
differences (genotype) with their surrounding 
environments. Genetic diversity both within species and 
among higher taxonomic groups can be assayed directly by 
surveying the actual genetic material (i.e. the genotype). 
The genetic diversity occurs in the form of nucleotide 
variation within the genome. When this variation causes a 
change in a given protein, the variants are termed alletes. 
Allelic variation occurs at various genetic loci, or gene 
positions within a chromosome. Genetically variable loci 
are termed polymorphic or are said to show polymorphism. 
Genetic diversity can also be assayed indirectly by 
measuring a phenol vpc with a presumed or demonstrated 
underlying genetic basis (Figure 2,2-1). As one moves up 
the taxonomic hierarchy, genetic diversity tends to increase 
with increasing taxonomic diversity, both within 
organismal groups (Figure 2.2-2<i) and across groups as a 
whole (Figure 2.2-lk]. 
The recognition that natural populations have high levels 
of genetic variation is something comparatively recent and 
followed from the application of allozyme electrophoresis 
to population genetics (Hubby and Lewontin 1966). This 
resulted in debate as to the factors responsible for the 
maintenance of these high levels of variation; the 
'neutralists' claimed that genetic variation accumulated 
through mutation to form new alleles, which remained in